10-K/A 1 form10ka07380_06302009.htm form10ka07380_06302009.htm
UNITED STATES
SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549
______________

FORM 10-K/A

(Amendment No. 1)


(Mark One)
x
ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
 
EXCHANGE ACT OF 1934

For the fiscal year ended June 30, 2009

¨
TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
 
SECURITIES EXCHANGE ACT OF 1934

For the Transition Period from ________ to ________

Commission File Number 000-26658

PHARMACYCLICS, INC.
(Exact Name of Registrant as Specified in its Charter)
   
DELAWARE
94-3148201
(State or other jurisdiction of
(I.R.S. Employer
incorporation or organization)
Identification No.)
   
995 E. Arques Avenue
  
Sunnyvale, California
94085-4521
(Address of principal executive offices)
(Zip code)
   
Registrant’s telephone number, including area code:  (408) 774-0330

Securities registered pursuant to Section 12(b) of the Act:

 
Name of each exchange on
Title of each class
which registered
Common Stock, $0.0001 par value
NASDAQ Capital Market

Securities registered pursuant to Section 12 (g) of the Act: None

Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act.  o Yes   x No

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act.  o Yes   x No
 

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.  x Yes   o No

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§ 229.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).  o Yes   o No

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of the registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K. o

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company.  See definition of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act.  (Check one):

Large Accelerated Filer  o
Accelerated Filer o
   
Non-Accelerated Filer  o
Smaller Reporting Company x

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).  o Yes   x No

The aggregate market value of the voting and non-voting stock held by non-affiliates of Registrant was $14,607,373 based on the closing sales price of the Registrant’s common stock on the NASDAQ Stock Market LLC on the last business day of the Registrant’s most recently completed second fiscal quarter.  Shares of the Registrant’s common stock beneficially owned by each executive officer and director of the Registrant and by each person known by the Registrant to beneficially own 10% or more of its outstanding common stock have been excluded, in that such persons may be deemed to be affiliates.  The determination of affiliate status is not necessarily a conclusive determination for other purposes.

On October 20, 2009, there were approximately 50,054,582 shares of common stock, par value $0.01 per share.

DOCUMENTS INCORPORATED BY REFERENCE

None.
 
 
EXPLANATORY NOTE
 
The purpose of this Amendment No. 1 on Form 10-K/A (the “Amendment”) is to amend and restate Part III, Items 10 through 14, of the previously filed Annual Report on Form 10-K of Pharmacyclics, Inc. (“Pharmacyclics” or the “Company”) for the year ended June 30, 2009, filed with the Securities and Exchange Commission on September 22, 2009 (the “Original Form 10-K”), to include information previously omitted in reliance on General Instruction G to Form 10-K, which provides that registrants may incorporate by reference certain information from a definitive proxy statement prepared in connection with the election of directors. The Company has determined to include such Part III information by amendment of the Original Form 10-K rather than by incorporation by reference to the proxy statement.  Accordingly, Part III of the Original Form 10-K is hereby amended and restated as set forth below.
 
There are no other changes to the Original Form 10-K other than those set forth below.  This Amendment does not reflect events occurring after the filing of the Original Form 10-K, nor does it modify or update disclosures therein in any way other than as required to reflect the amendment set forth below.  Among other things, forward-looking statements made in the Original Form 10-K have not been revised to reflect events that occurred or facts that became known to us after the filing of the Original Form 10-K, and such forward-looking statements should be read in their historical context.
 
______________________________________________
 
 
 
Annual Report on Form 10-K/A
 
For the Year Ended June 30, 2009
 
PAGE
 
 


 

Directors, Executive Officers and Corporate Governance
 
Set forth below are the names and ages of the directors and executive officers of the Company and their principal occupations at present and for the past five years.  The directors of the Company are elected to serve until the next annual meeting of stockholders and until their respective successors have been duly elected and qualified.  Our executive officers are appointed by the Board of Directors of the Company and serve until their successors have been duly appointed and qualified.  There are, to the knowledge of the Company, no agreements or understandings by which these individuals were so selected.  No family relationships exist between any directors or executive officers, as such term is defined in Item 402 of Regulation S-K promulgated under the Securities Exchange Act of 1934, as amended (the “Exchange Act”).  The Board has adopted independence standards for directors that conform to the standards required by the NASDAQ Stock Market (“NASDAQ”) for listed companies.  Based on the Company’s director independence standards, the Board has affirmatively determined that all of its directors other than Robert W. Duggan and Glenn C. Rice Ph.D. are independent.
 
Name
  
Age
  
Position(s) with the Company
  
Director Since
Robert W. Duggan
  
65
  
Director, Chairman and CEO
  
2007
Glenn C. Rice, Ph.D.(1)
  
53
  
Director, President and COO
  
2008
Jason T. Adelman
  
40
  
Director
  
2009
Cynthia C. Bamdad, Ph.D.
  
56
  
Director
  
2008
Minesh P. Mehta, M.D.
  
51
  
Director
  
2008
David D. Smith, Ph.D.
  
38
  
Director
  
2008

(1)
Dr. Rice will end his position with the Company effective mid-February, 2010.
 
Business Experience of Directors
 
Mr. Duggan has been a member of our Board of Directors since September 2007 and has served as Chief Executive Officer since September 2008. Mr. Duggan served as Chairman of the Board of Directors of Computer Motion, Inc., a computerized surgical systems company, from 1990 to 2003 and Chief Executive Officer from 1997. Computer Motion was acquired by Intuitive Surgical, Inc. in 2003. Mr. Duggan is the founder of the investment firm Robert W. Duggan & Associates. Mr. Duggan has been a private venture investor for more than 30 years and has participated as a director of, investor in, and advisor to numerous small and large businesses in the medical equipment, computer local and wide area network, PC hardware and software distribution, digital encryption, consumer retail goods and outdoor media communication industries. Mr. Duggan has also assisted in corporate planning, capital formation and management for his various investments.  He received the Congressman’s Medal of Merit and in 2000 he was named a Knight of the Legion of Honor by President Jacques Chirac. Mr. Duggan is currently also a director of Intuitive Surgical, Inc.  He is a member of the University of California at Santa Barbara Foundation Board of Trustees.
 
Dr. Rice has served as President and Chief Operating Officer of the company since February 2009 and became a director of Pharmacyclics in September of 2008.  Dr. Rice will end his position with the Company effective mid-February, 2010.  Dr. Rice has over 25 years of oncology drug development experience in the biopharmaceutical industry including research, preclinical and clinical trials as well as extensive experience in licensing, partnerships and M&A. Dr. Rice is the founder and served as Chief Executive Officer (CEO) of Pacific Biopharma Group from 2007 to 2009 and from 2004 to May 2007 as Founder and CEO of Bridge Laboratories, Inc.  From 2002 to 2004, Dr. Rice served as Vice President, Biosciences at SRI International in Menlo Park, CA, heading up a staff of 170 employees. In 2005, he helped co-found the Critical Path Institute, in Tucson, Arizona, a not-for-profit institute. From 1999 to 2002, Dr. Rice served as a Director and Vice President of Research at ILEX Oncology Inc., a NASDAQ listed oncology focused company. He was a founder and served as Chief Executive Officer and President in 1999 of Convergence Pharmaceuticals, Inc., a privately held Boston based cancer biopharmaceutical company which was sold to ILEX Oncology in 1999. Prior to Convergence, Dr. Rice was Vice President of Research at Cytokine Networks from 1998 to 1999, managing multiple preclinical and clinical programs and closing strategic partnerships; and Director of Cell Therapeutics (NASDAQ: CTIC) from 1993 to 1998.  He headed a discovery laboratory at Genentech Inc. (NYSE:DNA) from 1987 to 1993. Dr. Rice is currently an inventor on over 20 patents or patent applications and has authored over 75 manuscripts and book chapters.
 
 
Mr. Adelman was elected as a Director of the company in March 2009. Mr. Adelman is Senior Managing Director of Burnham Hill Partners LLC ("BHP"), an investment and merchant banking firm headquartered in New York City, which he founded in August of 2003. From September 1999 until July 2003 Mr. Adelman was Managing Director of Investment Banking in the New York office of H.C. Wainwright & Company, Inc. Mr. Adelman began his career at Coopers and Lybrand LLP where he worked in the financial services industry consulting practice, with a particular focus on the hedge fund industry. Mr. Adelman is also the co-founder and a Managing Member of Cipher Capital Partners since 2006. Mr. Adelman graduated from the University of Pennsylvania with a BA, cum laude, in Economics (1991) and graduated from Cornell Law School (1994), where he was Editor of the Cornell International Law Journal. Mr. Adelman also serves on the audit and compensation committees of Trio-Tech International, an Amex listed company.
 
Dr. Bamdad was elected as a Director of the company in October 2008. Dr. Bamdad has served as the Chairman of the Board, Chief Scientific Officer and Treasurer of Minerva Biotechnologies Corp. ("Minerva"), a pioneer in the field of nanotechnology, since 1999. She is the founder of Minerva and previously served as its Chief Executive Officer from 1999 to October 2005. She has also been a Director of the School of Social Science, Urban Affairs and Public Policy, Northeastern University since 2007. Dr. Bamdad received a B.S. in Physics from Northeastern University in 1992 and a Ph.D. in Biophysics from Harvard University in 1997. While a Ph.D. student at Harvard, Dr. Bamdad invented the first electronic DNA chip and the first universal protein chip. Dr. Bamdad is the sole or co-inventor of over 100 patent applications, both foreign and domestic, for novel technologies, therapeutics and diagnostics.
 
Dr. Mehta was elected as a Director of the company in September 2008. Dr. Mehta is an internationally recognized expert in human clinical drug trial strategy, design and execution and has managed national and international trials of all sizes including International Phase 3 trials. He is a Professor in the Department of Human Oncology at the University of Wisconsin's School of Medicine and Public Health since 2002, and is Program Leader of the Imaging and Radiation Sciences Program of the Paul P. Carbone Comprehensive Cancer Center (UWCCC). Dr. Mehta was Chairman of the Department of Human Oncology from 1997 to 2007. He has been a member of the Board of Directors of the American Society for Therapeutic Radiology and Oncology (ASTRO) since 2006 and Chair of the Radiation Therapy Oncology Group (RTOG) Brain Tumor Committee since 1998. From 1997 to 2001, he served as an ad-hoc member of the FDA's Technology Assessment Committee and from 2001 to 2005, he served on and eventually Chaired the FDA Radiological Devices Panel. He has more than 400 publications to his credit, especially in the areas of radiation therapy and translational and clinical cancer research. Dr. Mehta obtained his medical degree at the University of Zambia in 1981 and commenced his residency there at the Ndola Central Hospital. He moved to the University of Wisconsin, Madison, in 1984 and completed his residency in radiation oncology in 1988 when he took up an Assistant Professorship in Human Oncology, was promoted to Associate Professor and became the Director of the Radiation Oncology Residency Training Program. After serving as Vice-Chairman and Interim Chairman, Dr. Mehta became Chair of Human Oncology and also is a Professor in the Department of Neurological Surgery. Dr. Mehta currently serves as a Staff Physician at 8 hospitals in Wisconsin and Illinois. Dr. Mehta has authored over 70 clinical protocols.
 
Dr. Smith was elected as a Director of the company in October 2008. Dr. Smith has been a senior biostatistician at City of Hope, a cancer research hospital in Los Angeles since 2000. Dr. Smith holds a B.A. in Mathematics and a Ph.D. in Statistics. After his dissertation on integrating and synthesizing information in clinical and observational studies in oncology, he served as a Biostatistical Reviewer for the Division of Oncology Drug Products, U.S. Food and Drug Administration (FDA) for 3 years. During his tenure at the FDA, he reviewed more than 40 chemotherapy INDs and NDAs. He represented the FDA statistical perspective at five Oncologic Drugs Advisory Committee sessions, including three on the problems of missing data in outcomes research. After leaving the FDA in 2000, he went to City of Hope and the front lines of cancer research. During his eight years at City of Hope, he has designed and analyzed over 50 solid tumor and hematology protocols at all levels of development, from pre-clinical and genomic studies to Phase II/III trials. Dr. Smith has been a co-investigator on grants from the National Cancer Institute, National Institutes of Health, the American Cancer Society, the Susan G. Komen Breast Cancer Foundation and the Leukemia-Lymphoma Society. Dr. Smith is an author and coauthor of over 40 papers in peer-reviewed biostatistics, oncology, surgery, radiation, and immunology journals.
 
 
Executive Officers
 
Name
  
Age
  
Position
Robert W. Duggan
  
65
  
Chairman, Chief Executive Officer and Director
Glenn C. Rice, Ph.D.(1)
  
53
  
President, Chief Operating Officer and Director
Rainer M. Erdtmann
  
46
  
Vice President, Finance and Administration
and Secretary
Joseph J. Buggy, Ph.D.
  
42
  
Vice President, Research
Ahmed Hamdy, M.D.
  
44
  
Chief Medical Officer
David J. Loury, Ph.D.
  
53
  
Vice President, Preclinical Sciences

(1)
Dr. Rice will end his position with the Company effective mid-February, 2010.
 
Mr. Erdtmann has served as Vice President, Finance and Administration and Corporate Secretary since February 2009.  Since 2002, he served as a managing director of Oxygen Investments, LLC, a manager of equity and real estate funds that he co-founded in December 2002. Prior to co-founding Oxygen, Mr. Erdtmann co-founded a real estate development company in Europe and was responsible for building up its organization and overseeing its finance division.  Mr. Erdtmann began his career in investment banking with Commerzbank in Frankfurt, Germany, and later joined Commerz International Capital Management as a portfolio manager for international clients.  He graduated with distinction from the Westfaelische Wilhelms Universitaet in Muenster, majoring in finance and banking.
 
Dr. Buggy has served as Vice President, Research since September 2007. From May 2006 to August 2007, Dr. Buggy served as Senior Director, Cancer Biology. From November 2001 to April 2006, he served as Director, Department of Biology at Celera Genomics, a biotechnology company. From June 1996 to October 2001, he was a staff scientist at AXYS Pharmaceuticals, Inc., a biotechnology company. Prior to that Dr. Buggy worked as a scientist at Bayer Corporation in West Haven, CT. Dr. Buggy received a Ph.D. in Molecular, Cellular, and Developmental Biology from Indiana University and a B.S. degree in Microbiology from the University of Pittsburgh.
 
Dr. Hamdy has served as Chief Medical Officer since March of 2009. From July 2008 to February 2009, Dr. Hamdy served as Therapeutic Area Head at Elan Pharmaceuticals responsible for gastroenterology and autoimmune clinical development. Dr. Hamdy has also served as the General Medicine Therapeutic Area Head at PDL BioPharma from February 2006 to June 2008. From September 2004 to February 2006, Dr. Hamdy was a medical director at Johnson and Johnson/ALZA. From October 2000 to August 2004, Dr. Hamdy was a Senior Principal Scientist at Watson Pharmaceuticals. Dr. Hamdy received his M.D. (M.B.B.Ch) from Cairo University, Egypt.
 
Dr. Loury has served as Vice President, Preclinical Sciences since May 2006.  From April 2003 to May 2006, Dr. Loury served as Senior Director, Toxicology with Celera Genomics, a biotechnology company.  From June 2001 to April 2003, he was employed by Essential Therapeutics, Inc., a pharmaceutical company, as Director, Pharmacology and Toxicology.  From 1996 to 2001, Dr. Loury was employed by IntraBiotics Pharmaceuticals, Inc., most recently as Senior Director, Preclinical Development.  From 1986 to 1996 he worked in a variety of toxicology positions with Syntex/Roche Bioscience.  Dr. Loury received a Ph.D. in Pharmacology and Toxicology and a B.S. in Bio-Environmental Toxicology from the University of California, Davis.
 
 
Section 16(a) Beneficial Ownership Reporting Compliance
 
Section 16(a) of the Exchange Act requires the Company's directors and Section 16 officers, and persons who beneficially own more than 10% of a registered class of the Company's equity securities, to file with the Commission initial reports of beneficial ownership and reports of changes in beneficial ownership of Common Stock and other equity securities of the Company. Such officers, directors and greater than 10% stockholders are required by SEC regulations to furnish the Company with copies of all Section 16(a) reports they file.
 
Based solely on its review of the copies of such forms furnished to the Company and written representations that no other reports were required, the Company believes that, during the period from July 1, 2008 to June 30, 2009, all officers, directors and beneficial owners of more than 10% of the outstanding Common Stock complied with all Section 16(a) requirements, with the exception of the following late filings: (a) Dr. Rice was late filing one Form 3 and one Form 4 and (b) Dr. Mehta was late filing one Form 3 and one Form 4.
 
Code of Ethics and Committee Charters
 
The Board has also adopted a formal code of conduct that applies to all of our employees, officers and directors. The latest copy of our Code of Business Conduct and Ethics, as well as the Charters of the Audit Committee, the Compensation Committee and the Nominating and Corporate Governance Committee of the Board are available in the “Investors” section of our website at www.pharmacyclics.com.  Any person may obtain a copy of the Code of Business Conduct and Ethics, without charge, by writing to Pharmacyclics, Inc., 995 East Arques Avenue, Sunnyvale, California 94085, Attn: Secretary.
 
Audit Committee
 
The primary purpose of the Audit Committee is to oversee the accounting and financial reporting processes of the Company and the audits of the financial statements of the Company. The Audit Committee is also charged with the review and approval of all related party transactions involving the Company. The Audit Committee acts pursuant to a written charter that has been adopted by the Board. A more complete description of the powers and responsibilities delegated to the Committee is set forth in the Audit Committee charter. The Board had determined that all members of the Audit Committee, Jason T. Adelman, Cynthia C. Bamdad, Ph.D. and Minesh P. Mehta, M.D., for the fiscal year ended June 30, 2009, were “independent” as that term is defined in Rule 4200(a)(15) of the Nasdaq Marketplace Rules. The Board has determined that Mr. Adelman, the Audit Committee Chairman, is the “audit committee financial expert” as defined by Item 407(d)(5) of Regulation S-K of the Securities Act of 1933, as amended (the “Securities Act”).  The Audit Committee held five (5) meetings during the fiscal year ended June 30, 2009.
 
Executive Compensation
 
Tax Considerations
 
Section 162(m) of the Internal Revenue Code, enacted in 1993, generally disallows a tax deduction to publicly held companies for compensation exceeding $1 million paid to certain of the corporation's executive officers. The limitation applies only to compensation that is not considered to be performance-based. The non-performance-based compensation to be paid to the Company's executive officers for the 2009 fiscal year did not exceed the $1 million limit per officer, nor is it expected that the non-performance-based compensation to be paid to the Company's executive officers for fiscal 2010 will exceed that limit. The 2004 Plan is structured so that any compensation deemed paid to an executive officer in connection with the exercise of options granted under that plan with an exercise price equal to the fair market value of the option shares on the grant date will qualify as performance-based compensation, which will not be subject to the $1 million limitation. Because it is very unlikely that the cash compensation payable to any of the Company's executive officers in the foreseeable future will approach the $1 million limit, the Compensation Committee has decided at this time not to take any other action to limit or restructure the elements of cash compensation payable to the Company's executive officers. The Compensation Committee will reconsider this decision should the individual compensation of any executive officer approach the $1 million level.
 
 
Severance and Change in Control Arrangements
 
The Company’s 2004 Plan provides that 50% of all unvested options shall become fully vested upon a change in control of the Company. The plan further provides that if the employee’s employment is terminated within twelve (12) months of a change in control, the remaining balance of unvested options shall become fully vested.
 
The Company has entered into a severance agreement with Dr. Loury under which Dr. Loury will be paid on year’s base salary upon his involuntary termination, provided such termination is not for cause, as defined in the agreement.
 
Separation Agreements
 
Richard Miller, the Company’s former president and chief executive officer, resigned from such positions effective September 10, 2008.  In connection with Dr. Miller’s resignation, the Company and Dr. Miller entered into a separation agreement, dated September 12, 2008, whereby the Company agreed to (i) pay Dr. Miller one year of salary in severance payments, a portion of which was paid in the same intervals and amounts as his regular paycheck from the date following the termination of his employment with the Company until the end of the 2008 calendar year, and the remainder of which was paid in a lump sum payment on January 2, 2009, (ii) accelerate vesting of all of Dr. Miller’s outstanding options on October 1, 2008 with each option expiring on October 1, 2011 and (iii) provide health care benefits to Dr. Miller for 12 months following the termination of his employment with the Company.  In exchange, Dr. Miller agreed to cooperate with the Company in providing a smooth and orderly transition of his former job responsibilities to other employees of the Company until the end of the 2008 calendar year and to release the Company from any and all claims that legally can be released.
 
Leiv Lea, the Company’s former vice presdient, finance and administrator and secretary, resigned from such positions effective October 31, 2008.  In connection with Mr. Lea’s resignation, the Company and Mr. Lea entered into a separation agreement, dated September 12, 2008, whereby the Company agreed to (i) pay Mr. Lea one year of salary in severance payments, a portion of which was paid in the same intervals and amounts as his regular paycheck from the date following the termination of his employment with the Company until the end of 2008 calendar year, and the remainder of which was paid in a lump sum payment on January 2, 2009, (ii) accelerate vesting of all of Mr. Lea’s outstanding options on November 1, 2008 with each option expiring on November 1, 2011, and (iii) provide health care benefits to Mr. Lea for 12 months following the effective date of his resignation.  In exchange, Mr. Lea agreed to cooperate with the Company in providing a smooth and orderly transition of his former job responsibilities to other employees of the Company until the end of 2008 calendar year and to release the Company from any and all claims that legally can be released.
 
Retirement Plans
 
We maintain a 401(k) Plan that is a defined contribution plan intended to qualify under Section 401(a) of the Internal Revenue Code of 1986, as amended.  In fiscal 2009, the Company matched 50% of all participant contributions up to a maximum of $1,500 per employee.  The Company does not maintain a defined benefit pension plan or a nonqualified deferred compensation plan.
 
 
Summary Compensation Table
 
The following table sets forth all compensation awarded to, paid or earned by the following type of executive officers for each of the Company’s last two completed fiscal years: (i) individuals who served as, or acted in the capacity of, the Company’s principal executive officer for the fiscal year ended June 30, 2009; (ii) the Company’s two most highly compensated executive officers, other than the chief executive, who were serving as executive officers at the end of the fiscal year ended June 30, 2009; and (iii) up to two additional individuals for whom disclosure would have been provided but for the fact that the individual was not serving as an executive officer of the Company at the end of the fiscal year ended June 30, 2009 (of which there were two).  We refer to these individuals collectively as our named executive officers.
 
           
Option
  
All Other
      
 
  
Fiscal
  
Salary
  
Awards
  
Compensation
  
 
  
Name and Principal Position
  
Year
  
($) (1)
  
($) (2)
  
($)
    
Total ($)
Robert W. Duggan (3)
  
2009
  
              -
  
                    -
  
                    -
    
                 -
Chairman and Chief Executive Officer
                      
                       
Joseph J. Buggy, Ph.D.
  
2009
  
  192,115
  
          88,605
  
             1,500
 (4)
  
     282,220
Vice President, Research
  
2008
  
  181,714
  
          66,434
  
                    -
    
     248,148
                       
David J. Loury, Ph.D.
  
2009
  
  265,215
  
        129,111
  
             1,500
 (4)
  
     395,826
Vice President, Preclinical Sciences
  
2007
  
  210,000
  
          80,927
  
             1,500
 (4)
 
     292,427
                       
Richard A. Miller, M.D. (5)
  
2009
  
  121,562
  
        109,685
  
      1,736,092
 (6)
  
  1,967,339
   
2008
  
  438,973
  
        645,273
  
             1,500
 (4)
  
  1,085,746
                       
Leiv Lea (7)
  
2009
  
    97,484
  
          45,733
  
         911,544
 (8)
  
  1,054,761
   
2008
  
  257,584
  
        260,478
  
             1,500
 (4)
  
     519,562
 
(1)
Includes amounts earned but deferred at the election of the Named Executive Officer, such as salary deferrals under the Company's 401(k) plan.
(2)
The Company's share-based compensation program includes incentive and non-statutory stock options. Amounts reflect the dollar amount recognized for financial statement reporting purposes, in accordance with Statement of Financial Accounting Standards (“SFAS”) No. 123, Share-Based Payment and thus include amounts from outstanding stock option awards granted in and prior to the indicated fiscal year, as applicable.  Assumptions used in the calculation of these amounts are disclosed in Note 1 to the Company’s Financial Statements for the fiscal year ended June 30, 2009 included in the Company’s Annual Report on Form 10-K filed with the Securities and Exchange Commission on September 22, 2009.  However, as required, amounts exclude the impact of estimated forfeitures related to service-based vesting conditions
(3)
Mr. Duggan has declined any compensation from the Company.  Mr. Duggan became the Company’s Interim Chief Executive Officer on September 10, 2008 and became the Company’s Chief Executive Officer on February 12, 2009.
(4)
Consists of the Company’s matching contribution under its 401(k) plan.
(5)
Dr. Miller resigned his position as President and Chief Executive Officer effective September 10, 2008.
(6)
Consists of cash severance payments of $438,973, stock compensation expense of $1,207,841 associated with the acceleration of vesting and extension of the exercise period of Dr. Miller’s options pursuant to his severance agreement, payment of accrued paid time-off of $75,976, payment of COBRA insurance premiums of $11,802 and a $1,500 Company matching contribution under its 401(K) plan.
(7)
Mr. Lea resigned his position as Vice President, Finance and Administration and Secretary effective October 31, 2008.
(8)
Consists of cash severance payments of $267,883, stock compensation expense of $583,995 associated with the acceleration of vesting and extension of the exercise period of Mr. Lea’s options pursuant to his severance agreement, payment of accrued paid time-off of $46,364, payment of COBRA insurance premiums of $11,802 and a $1,500 Company matching contribution under its 401(K) plan.
 
 
Outstanding Equity Awards at 2009 Fiscal Year-End
 
The following table provides information on the current holdings of stock options by the named executives. Each option grant is shown separately for each named executive. The vesting schedule for each option grant is shown following this table.
 
   
Option Awards
  
   
Number of Securities
          
Number of Securities
    
Option
        
   
Underlying
          
Underlying
    
Exercise
    
Option
  
   
Unexercised Options
          
Unexercised Options
    
Price
    
Expiration
  
Name
  
Exercisable
          
Un-exercisable
    
($)
    
Date
  
Robert W. Duggan
     -             -       -       -  
Joseph J. Buggy, Ph.D.
     54,000       (1 )     -       4.16    
05/23/16
  
      30,000       (2 )     -       2.76    
03/13/17
  
      40,000       (2 )     -       2.44    
09/17/17
  
      54,687       (2 )     70,313       0.86    
03/18/18
  
      -       (3 )     151,000       0.75    
03/03/19
  
David J. Loury, Ph.D.
     65,000       (1 )     -       4.16    
05/23/16
  
      32,812       (2 )     42,188       2.76    
03/13/17
  
      54,687       (2 )     70,313       0.86    
03/18/18
  
      62,961       (4 )     137,039       1.35    
11/04/18
  
      -       (3 )     100,000       0.75    
03/03/19
  
Richard A. Miller, M.D.
     75,000       (5 )     -       58.06    
06/06/10
  
      114,000       (5 )     -       27.51    
05/25/11
  
      120,000       (5 )     -       7.39    
10/01/11
  
      84,000       (5 )     -       4.25    
10/01/11
  
      80,000       (5 )     -       5.25    
10/01/11
  
      40,000       (5 )     -       7.10    
10/01/11
  
      61,000       (5 )     -       11.21    
10/01/11
  
      175,000       (5 )     -       7.76    
10/01/11
  
      250,000       (5 )     -       4.16    
10/01/11
  
      210,000       (5 )     -       2.76    
10/01/11
  
      275,000       (5 )     -       0.86    
10/01/11
  
Leiv Lea
     20,000       (5 )     -       58.06    
06/06/10
  
      50,000       (5 )     -       27.51    
05/25/11
  
      40,000       (5 )     -       7.39    
11/01/11
  
      40,000       (5 )     -       4.25    
11/01/11
  
      55,000       (5 )     -       4.47    
11/01/11
  
      32,250       (5 )     -       11.21    
11/01/11
  
      60,000       (5 )     -       7.76    
11/01/11
  
      110,000       (5 )     -       4.16    
11/01/11
  
      110,000       (5 )     -       2.76    
11/01/11
  
      150,000       (5 )     -       0.86    
11/01/11
  
 
(1)
25% of the shares subject to the option vest on the one year anniversary of the date of grant and the remaining shares subject to the option vest in a series of 36 equal and successive monthly installments thereafter.
(2)
Each of the options vest in forty-eight (48) equal installments beginning on the date of grant.
(3)
Option vests in four equal annual installments beginning March 3, 2010, subject to the satisfaction of certain performance criteria with respect to each annual period.
(4)
Option vests in a series of five equal and successive annual installments measured from November 4, 2008.
(5)
Options are fully vested.
 
None of our Named Executive Officers exercised any of his stock options in fiscal 2009 and as a result, there was no value realized.
 
 
DIRECTOR COMPENSATION
 
Cash Compensation
 
Prior to October 10, 2008, the Company’s non-employee directors received a quarterly retainer of $3,750 and a payment of $1,000 for attending each meeting of the Board.  Committee chairmen received an additional $1,000 per Committee meeting attended.
 
The Board amended the compensation of its non-employee directors for services subsequent to October 10, 2008.  Following such date, each non-employee director received $30,000 per annum for their Board service, payable quarterly, and $500 for each Board committee meeting attended.  Each committee chairman received $1,000 (instead of $500) for each Board committee meeting attended.  Board members may elect to receive their compensation in the form of non-qualified stock options with a face value equal to three (3) times the amount of cash compensation earned.
 
Equity Compensation
 
Each non-employee Director receives an automatic option grant to purchase 10,000 shares on the day they become a member of the Board with an exercise price of one hundred (100%) of the fair market value on the date of grant (“Initial Option”).  Each non-employee Director of the Company receives an annual automatic grant on the day of the Company’s Annual Meeting of a non-qualified stock option to purchase 7,500 shares with an exercise price of one hundred (100%) of the fair market value on the date of grant (“Annual Replenishment Option”), providing that the Director has served as a Director for at least the six (6) months prior to the Annual Meeting.
 
All Director option grants are nonstatutory stock options subject to the terms and conditions of the 2004 Plan.  Each Initial Option vests at the rate of 1/60th per month over sixty (60) months from the date of grant of the Initial Option, and each Annual Replenishment Option vests at the rate of 1/12th per month over twelve (12) months from the date of grant of the Annual Replenishment Option.  Furthermore, Initial Options and Annual Replenishment Options vest only during the optionholder’s service as a Board member; provided however, that the Compensation Committee has the power to accelerate the time during which an option granted to a Director may vest.
 
Initial Options and Annual Replenishment Options terminate upon the earlier of (i) ten (10) years after the date of grant or (ii) thirty-six (36) months after the date of termination of the optionholder’s service as a Board member.
 
During the fiscal year ended June 30, 2009, Mr. Adelman, Dr. Bamdad, Dr. Mehta, Dr. Rice and Dr. Smith each received Initial Options to acquire 10,000 shares of common stock at exercise prices of $0.91, $1.92, $2.30, $2.30, and $1.92, per share, respectively.
 
 
The following table sets forth the compensation earned or awarded to the Company’s non-employee directors during the fiscal year ended June 30, 2009.
 
 
   
Fees Earned or
              
   
Paid in Cash
    
Option Awards
    
Total
  
Current Directors:
  
($) (1)
    
($) (2)
    
($)
  
Robert W. Duggan
     -       -       -  
Jason T. Adelman
     18,500       23,467       41,967  
Cynthia C. Bamdad, Ph.D.
     24,000       34,271       58,271  
Minesh P. Mehta, M.D.
     36,250       2,430       38,680  
Glenn C. Rice, Ph.D.(3)
     18,750       41,249       59,999  
David D. Smith, Ph.D.
     30,500       49,617       80,117  
Former Directors:
                        
Miles R. Gilburne
     5,750       27,102       32,852  
James L. Knighton
     23,250       74,509       97,759  
Richard M. Levy, Ph.D.
     4,750       19,226       23,976  
Christine A. White, M.D.
     5,750       21,319       27,069  
                         
 
(1)
See the section entitled “Director Compensation - Cash Compensation”, above, for a description of the cash compensation program for the Company’s non-employee directors during the fiscal year ended June 30, 2009. Amounts earned in one year and paid in the following year are, for purposes on this table only, accounted for in the year earned. Includes fees with respect to which directors elected to receive option shares in lieu of such fees. The following directors received option shares in the amounts set forth below in lieu of the fees set forth below (includes fees forgone earned in the fourth quarter of fiscal 2009 where the related options were granted the first day of fiscal 2010):
 
 
 
Current Directors:
  
 
Fees Forgone
    
Option Shares
Received in Lieu
Of Cash
  
Jason T. Adelman
   $ 18,500       50,593  
Cynthia C. Bamdad, Ph.D.
     24,000       76,871  
Glenn C. Rice, Ph.D.
     18,750       60,836  
David D. Smith, Ph.D.
     30,500       92,020  
Former Directors:
                
Miles R. Gilburne
     5,750       8,097  
James L. Knighton
     23,250       70,616  
Richard M. Levy, Ph.D.
     3,750       5,281  
Christine A. Whilte, M.D.
     2,875       4,049  
 
(2)
Amounts reflect the dollar amount recognized for financial statement reporting purposes for the fiscal year ended June 30, 2009, in accordance with Statement of Financial Accounting Standards (“SFAS”) No. 123, Share-Based Payment, and include amounts attributable to awards granted in and prior to fiscal 2008. Assumptions used in the calculation of these amounts are disclosed in Note 1 to the Company’s Financial Statements for the fiscal year ended June 30, 2009 included in the Company’s Annual Report on Form 10-K filed with the Securities and Exchange Commission on September 22, 2009. However, as required, amounts exclude the impact of estimated forfeitures related to service-based vesting conditions. See the section entitled “Director Compensation - Equity Compensation”, above, for a description of the Company’s cash compensation policy for non-employee directors and the specific terms of the stock options granted to the Company’s non-employee directors during the fiscal year ended June 30, 2009. The grant date fair value of option awards granted in fiscal year 2009 is as follows:
 
 
Current Directors:
Grant
Date
  
Grant
Date
Fair Value
  
Jason T. Adelman
02/05/09
   $ 6,521  
 
04/01/09
     22,949  
        29,470  
Cynthia C. Bamdad, Ph.D.
10/09/08
     12,659  
 
01/02/09
     32,440  
        45,009  
Minesh P. Mehta, M.D.
09/10/08
     15,138  
        15,138  
Glenn C. Rice, Ph.D.
09/10/08
     15,138  
 
10/01/08
     7,425  
 
01/02/09
     31,394  
        53,957  
David D. Smith, Ph.D.
10/09/08
     12,659  
 
01/02/09
     31,394  
 
04/01/09
     16,392  
        60,445  
Former Directors:
          
Miles R. Gilburne
07/01/08
     11,262  
 
10/01/08
     11,384  
        22,646  
James L. Knighton
07/01/08
     13,222  
 
10/01/08
     13,365  
 
12/12/08
     6,168  
 
01/02/09
     34,533  
        67,288  
Richard M. Levy, Ph.D.
07/01/08
     7,345  
 
10/01/08
     7,425  
        14,770  
Christine A. Whilte, M.D.
07/01/08
     5,631  
 
10/01/08
     5,693  
        11,324  
 
The aggregate number of stock options outstanding as of June 30, 2009 is as follows: 35,403 shares for Mr. Adelman, 67,406 shares for Dr. Bamdad, 10,000 shares for Dr. Mehta, 83,700 shares for Dr. Smith, 166,988 shares for Mr. Gilburne, 166,311 shares for Mr. Knighton, 118,452 shares for Dr. Levy, and 49,863 shares for Dr. White. There were no options that were repriced or otherwise materially modified during fiscal year 2008. Mr. Gilburne, Mr. Knighton, Dr. Levy and Dr. White forfeited 2,500, 12,875, 2,500 and 8,500 options, respectively, associated with their resignations as Board Members.
 
(3)
Represents compensation earned by Dr. Rice prior to his appointment as President and Chief Operating Officer in March 2009.  Dr. Rice will end his position with the Company effective mid-February, 2010.
 
 
Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters
 
Securities Authorized for Issuance Under Equity Compensation Plans
 
The table below shows, as of June 30, 2009, information for all equity compensation plans previously approved by stockholders and for all compensation plans not previously approved by stockholders.
 
Equity Compensation Plan Information
 
               
Number of securities
  
               
remaining available
  
   
Number of securities
          
for future issuance
  
   
to be issued
    
Weighted-average
    
under equity
  
   
upon exercise of
    
exercise price of
    
compensation plans
  
   
outstanding options,
    
outstanding options,
    
(excluding securities
  
   
warrants and rights
    
warrants and rights
    
reflected in column (a))
  
Plan Category
  
(a)
    
(b)
    
(c) (1)
  
Equity compensation plans
                  
    approved by security holders (2)
     8,452,899     $ 4.94       1,122,956  
Equity compensation plans not
                        
    approved by security holders
     -       -       -  
Total
     8,452,899     $ 4.94       1,122,956  
 
_______________

(1)           Includes approximately 478,572 shares issuable under the Company's Employee Stock Purchase Plan.

(2)           Includes our:
 
·
2004 Equity Incentive Award Plan
 
·
1995 Stock Option Plan
 
·
1995 Non-Employee Director Stock Option Plan
 
·
Employee Stock Purchase Plan

Security Ownership of Certain Beneficial Owners and Management
 
The following table sets forth certain information regarding the beneficial ownership of the Company's Common Stock as of September 30, 2009, by: (i) each stockholder who, based on publicly available records, is known by the Company to own beneficially more than five percent (5%) of the Company's Common Stock; (ii) each current director; (iii) each executive officer named in the "Summary Compensation Table" below (the "Named Executive Officers"); and (iv) all current directors and executive officers of the Company as a group. The address for each director and executive officer listed in the table below is c/o: Pharmacyclics, Inc., 995 East Arques Avenue, Sunnyvale, California 94085.
 
 

   
Beneficial Ownership (1)
  
         
Shares Issuable
        
         
Pursuant to
        
   
Outstanding
    
Options Vested
        
   
Shares of
    
and Exercisable
    
Percent of
  
   
Common
    
Within 60 Days of
    
Total Shares
  
Name
  
Stock
    
September 30, 2009
    
Outstanding
  
Federated Investors, Inc. (2)
     4,154,098       -       8.3 %
Jason T. Adelman
     -       50,593       *  
Cynthia C. Bamdad
     -       78,871       *  
Joseph J. Buggy, Ph.D.
     5,000       141,000       *  
Robert W. Duggan (3)
     12,388,222       -       24.8 %
David J. Loury, Ph.D.
     -       198,958       *  
Minesh P. Mehta, M.D.
     -       2,000       *  
David D. Smith, Ph.D.
     2,000       94,020       *  
Richard A. Miller, M.D. (4)
     326,798 (5)     1,484,000       3.5 %
Leiv Lea (6)
     20,893 (7)     667,250       1.4 %
                         
All current executive officers and
                        
  directors as a group (10 persons)
     12,800,166       628,278       26.5 %
_______________

* Less than 1%.

(1)
Beneficial ownership is determined in accordance with the rules of the SEC and generally includes voting or investment power with respect to securities. Beneficial ownership also includes shares of stock subject to options which are vested and exercisable within sixty (60) days of the September 30, 2009 date of this table. Except as indicated by footnote, and subject to community property laws where applicable, to the knowledge of the Company, all persons named in the table above have sole voting and investment power with respect to all shares of Common Stock shown as beneficially owned by such holders. The percentages of beneficial ownership are based on 50,054,582 shares of Common Stock outstanding as of September 30, 2009, adjusted as required by rules promulgated by the Commission. For purposes of computing the percentage of outstanding shares held by each person or group of persons named above on a given date, any shares which such person or persons has the right to acquire within sixty (60) days after such date are deemed to be outstanding, but are not deemed to be outstanding for the purpose of computing the percentage ownership of any other person.
 
(2)
Derived from a Form 13G/A filed September 10, 2009.  The address of Federated Investors, Inc. is Federated Investors Tower, Pittsburgh, Pennsylvania, 15222
 
(3)
Mr. Duggan disclaims beneficial ownership of 649,112 shares held in managed accounts except to the extent of his pecuniary interest in those shares.
 
(4)
Dr. Miller resigned his position as President, Chief Executive Officer and a director effective September 10, 2008.
 
(5)
Based on a Form 4 filed March 20, 2008.
 
(6)
Mr. Lea resigned his position as Vice President, Finance and Administration and Secretary effective October 31, 2008.
 
(7)
Based on a Form 4 filed May 1, 2008.
 
 
Certain Relationships and Related Transactions, and Director Independence
 
 
Director Independence
 
The Board has determined that all of the members of the Board during the fiscal year ended June 30, 2009, other than Mr. Duggan and Dr. Rice were “independent” as that term is defined in the Nasdaq Marketplace Rules.  Mr. Duggan and Dr. Rice were not considered independent because each was an executive officer of the Company.  As required under applicable Nasdaq Marketplace Rules, the Company’s independent directors meet regularly in executive session at which only they are present.  Dr. Miller, who resigned as a director on September 10, 2008 was also not independent.
 
Our Board has an Audit Committee, a Compensation Committee and a Nominating and Corporate Governance Committee.  All directors attended at least 75% of the aggregate of all meetings of our Board and of the committees on which they served during the fiscal year ended June 30, 2009.  Current and former committee membership and the number of meetings of our full Board and Committees held in fiscal 2009 are shown in the table below:
 
               
Nominating and
               
Corporate
       
Audit
  
Compensation
  
Governance
Current Directors:
  
Board
  
Committee
  
Committee
  
Committee
Robert W. Duggan
  
Chairman
            
Glenn C. Rice, Ph.D.
  
Member
            
Jason T. Adelman
  
Member
  
Chair
  
Chair
  
Member
Cynthia C. Bamdad, Ph.D.
  
Member
  
Member
  
Member
  
Member
Minesh P. Mehta, M.D.
  
Member
  
Member
  
Member
  
Member
David D. Smith, Ph.D.
  
Member
          
Member
                 
Former Directors:
                
Miles R. Gilburne(1)
  
Member
  
Member
      
Member
James L. Knighton(2)
  
Member
  
Chair
      
Member
Richard M. Levy, Ph.D.(1)
  
Member
      
Chair
  
Member
Richard A. Miller, M.D.(1)
  
Member
            
Christine A. White, M.D.(1)
  
Member
  
Member
  
Member
  
Member
 
(1)
Resigned on September 10, 2008
 
(2)
Resigned on January 15, 2009
 
Loan to Company
 
In December 2008, the Company borrowed $5,000,000 and in March 2009, borrowed $1,400,000 from an affiliate of Robert W. Duggan, the Company’s Chairman of the Board and Chief Executive Officer.  Under the terms of the unsecured loans, the Company was to repay the principal sum of $6,400,000 on the earlier of (i) July 1, 2010 or (ii) upon the closing of an equity offering or rights offering by the Company.  The loans bore interest as follows: (i) 1.36% from December 30, 2008 until March 31, 2009, and (ii) the rate of interest in effect for such day as publicly announced from time to time by Citibank N.A. as its “prime rate” from April 1, 2009 until December 31, 2009.  Interest was to be paid annually.  The full $6,400,000 amount of the loans plus accrued interest was repaid in August 2009 in connection with July closing of the Company’s rights offering.
 
 
Principal Accountant Fees and Services
 
Pre-Approval Policy and Procedures
 
In accordance with the Audit Committee charter, the Audit Committee's policy is to pre-approve all audit and non-audit services provided by the independent registered public accounting firm, including the estimated fees and other terms of any such engagement. These services may include audit services, audit-related services, tax services and other services. Any pre-approval is detailed as to the particular service or category of services. The Audit Committee may elect to delegate pre-approval authority to one or more designated Committee members in accordance with its charter. The Audit Committee has delegated to Mr. Adelman, as Chairman, the ability to pre-approve certain audit and non-audit services. The Audit Committee considers whether such audit or non-audit services are consistent with the SEC's rules on auditor independence. The Audit Committee has considered whether the provision of the services noted above is compatible with maintaining PricewaterhouseCoopers LLP's independence.
 
Independent Registered Public Accounting Firm Fees
 
The following table sets forth the aggregate fees billed or to be billed by PricewaterhouseCoopers LLP for the following services during fiscal 2009 and 2008:
 
   
Fiscal 2009
    
Fiscal 2008
  
Audit fees
   $ 350,500     $ 265,500  
Audit-related fees
     -       -  
Tax fees
     56,500       30,000  
All other fees
     -       -  
Total
   $ 407,000     $ 295,500  

In the above table, "audit fees" for professional services for the audit of the Company's financial statements included in its Annual Report on Form 10-K for the years ended June 30, 2009 and 2008, and review of financial statements included in its quarterly reports on Form 10-Q and for services that are normally provided in connection with statutory and regulatory filings. "Tax fees" are fees for tax compliance, tax advice and tax planning. All fees described above were approved by the Audit Committee, pursuant to the pre-approved policy described below.
 
 
 
Exhibits and Financial Statement Schedules
 
1.           Financial Statements:
 
The required consolidated financial statements of the Company and the related report of the Company’s independent public accountants thereon were previously filed under Item 8 of the Original Form 10-K.
 
2.           Financial Statement Schedules:
 
The required financial statement schedules of the Company and the related report of the Company’s independent public accountants thereon were previously filed as schedules to the Original Form 10-K.
 
3.           Exhibits:
 
Exhibit Number
Description
   
3.1
Amended and Restated Certificate of Incorporation of the Company (incorporated by reference to Exhibit 3.1 to the Company’s Current Report on Form 8-K filed with the Securities and Exchange Commission on December 16, 2008).
   
3.2
Amended and Restated Bylaws of the Company (incorporated by reference to Exhibit of the same number to the Quarterly Report on Form 10-Q for the quarter ended December 31, 2001).
   
3.3
Amendment to the Amended and Restated Bylaws of the Company (incorporated by reference to Exhibit 3.1 to the Periodic Report on Form 8-K filed on August 9, 2006).
   
4.2
Specimen Certificate of the Company’s Common Stock (incorporated by reference to Exhibit 4.2 to the Company’s Registration Statement on Form S-1, Commission File No. 33-96048).
   
4.3*
Stock Purchase Agreement By and Between Pharmacyclics, Inc. and Applera Corporation dated April 7, 2006 (incorporated by reference to Exhibit 4.3 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2006).
   
4.5
Form of Stock Purchase Agreement related to the February 19, 2009 sale of approximately 1.5 million shares of the Company’s common stock to certain foreign and U.S. individuals and entities of which some are shareholders of Pacific Biopharma Group, Ltd. (incorporated by reference to Exhibit 4.1 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2009).
   
10.6*
Patent License Agreement entered into between the Company and The University of Texas, Austin entered into on or about July 1, 1991 (incorporated by reference to Exhibit 10.8 to the Company’s Registration Statement on Form S-1, Commission File No. 33-96048).
   
10.7*
Patent License Agreement entered into between the Company and The University of Texas, Dallas dated as of July 1, 1992, as amended by the Patent License Agreement dated May 27, 1993 (incorporated by reference to Exhibit 10.9 to the Company’s Registration Statement on Form S-1, Commission File No. 33-96048).
   
10.8*
Patent License Agreement entered into between the Company and Stuart W. Young dated as of October 15, 1992 (incorporated by reference to Exhibit 10.10 to the Company’s Registration Statement on Form S-1, Commission File No. 33-96048).
 
 
   
10.9
Lease Agreement entered into between the Company and New England Mutual Life Insurance Company dated as of June 17, 1993, as amended on July 22, 1993, and as further amended on March 1, 1994 (incorporated by reference to Exhibit 10.11 to the Company’s Registration Statement on Form S-1, Commission File No. 33-96048).
   
10.13+
The Company’s 1995 Stock Option Plan (incorporated by reference to Exhibit 99.1 to the Company’s Registration Statement on Form S-8, Commission File No. 333-52881).
   
10.14+
The Company’s 1995 Non-Employee Directors’ Stock Option Plan (incorporated by reference to Exhibit 99.7 to the Company’s Registration Statement on Form S-8, Commission File No. 33-98514).
   
10.15+
The Company’s Employee Stock Purchase Plan as amended on October 9, 2008 (incorporated by reference to Exhibit 10.2 to the Company’s Current Report on Form 8-K filed with the Securities and Exchange Commission on December 16, 2008).
   
10.16+
Employment Agreement entered into between the Company and Richard A. Miller, M.D. dated as of June 10, 1992 (incorporated by reference to Exhibit 10.19 to the Company’s Registration Statement on Form S-1, Commission File No. 33-96048).
   
10.22+
Form of Notice of Grant of Stock Option generally to be used under the 1995 Stock Option Plan (incorporated by reference to Exhibit 99.2 to the Company’s Registration Statement on Form S-8, Commission File No. 33- 98514).
   
10.23+
Form of Stock Option Agreement (incorporated by reference to Exhibit 99.3 to the Company’s Registration Statement on Form S-8, Commission File No. 333-52881).
   
10.25+
Form of Addendum to Stock Option Agreement (Special Tax Election) (incorporated by reference to Exhibit 99.5 to the Company’s Registration Statement on Form S-8, Commission File No. 33-98514).
   
10.26+
Form of Addendum to Stock Option Agreement (Involuntary Termination following Change in Control) (incorporated by reference to Exhibit 99.6 to the Company’s Registration Statement on Form S-8, Commission File No. 33- 98514).
   
10.27+
Form of Notice of Grant of Automatic Stock Option (Initial Grant) (incorporated by reference to Exhibit 99.8 to the Company’s Registration Statement on Form S-8, Commission File No. 33-98514).
   
10.28+
Form of Notice of Grant of Automatic Stock Option (Annual Grant) (incorporated by reference to Exhibit 99.9 to the Company’s Registration Statement on Form S-8, Commission File No. 33-98514).
   
10.29+
Form of Non-Employee Director Stock Option Agreement (incorporated by reference to Exhibit 99.10 to the Company’s Registration Statement on Form S-8, Commission File No. 33-98514).
   
10.30+
Form of Employee Stock Purchase Plan Enrollment/Change Form (incorporated by reference to Exhibit 99.12 to the Company’s Registration Statement on Form S-8, Commission File No. 33-98514).
   
10.31+
Form of Stock Purchase Agreement (incorporated by reference to Exhibit 99.13 to the Company’s Registration Statement on Form S-8, Commission File No. 33-98514).
 
 
   
10.38+
Employment Agreement, dated December 18, 1997, by and between the Company and Leiv Lea (incorporated by reference to Exhibit 10.38 to the Quarterly report on Form 10-Q for the quarter ended March 31, 1998).
   
10.44*
Master Development and Supply Agreement, dated March 20, 2000 by and between Cook Imaging Corporation, D.B.A. Cook Pharmaceutical Solutions, and the Registrant (incorporated by reference to Exhibit 10.1 to the Quarterly report on Form 10-Q for the quarter ended March 31, 2000).
   
10.47*
Supply Agreement, dated December 11, 2000 by and between Dixie Chemical Company and the Registrant (incorporated by reference to Exhibit 10.1 to the Quarterly Report on Form 10-Q for the quarter ended December 31, 2000).
   
10.48*
Supply Agreement, dated December 18, 2000 by and between Lonza, AG and the Registrant (incorporated by reference to Exhibit 10.2 to the Quarterly Report on Form 10-Q for the quarter ended December 31, 2000).
   
10.49
Lease and Lease Termination Agreement dated June 14, 2000 by and between the Registrant and Metropolitan Life Insurance Company (incorporated by reference to Exhibit 10.49 to the Annual Report on Form 10-K for the year ended June 30, 2001).
   
10.50
First Amendment to New Lease dated April 10, 2001 by and between the Registrant and Metropolitan Life Insurance Company (incorporated by reference to Exhibit 10.50 to the Annual Report on Form 10-K for the year ended June 30, 2001).
   
10.51
Second Amendment to New Lease dated June 29, 2001 by and between the Registrant and Metropolitan Life Insurance Company (incorporated by reference to Exhibit 10.51 to the Annual Report on Form 10-K for the year ended June 30, 2001).
   
10.53*
Supply Agreement, dated August 17, 2001 by and between EMS-Dottikon AG and the Registrant (incorporated by reference to Exhibit 10.1 to the Quarterly Report on Form 10-Q for the quarter ended September 30, 2001).
   
10.54
Third Amendment to New Lease dated February 5, 2003 by and between the Registrant and Metropolitan Life Insurance Company (incorporated by reference to Exhibit 10.1 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2003).
   
10.55
Form of Indemnification Agreement between the Company and its directors and executive officers (incorporated by reference to Exhibit 10.55 to the Annual Report on Form 10-K for the year ended June 30, 2004).
   
10.56+
The Company’s 2004 Equity Incentive Award Plan (the “2004 Plan”) as amended on October 9, 2008 (incorporated by reference to Exhibit 10.1 to the Company’s Current Report on Form 8-K filed with the Securities and Exchange Commission on December 16, 2008).
   
10.57+
Form of Option Agreement for the 2004 Plan (incorporated by reference from Exhibit 99.1 to the Company’s Current Report on Form 8-K filed with the Securities and Exchange Commission on December 22, 2004).
   
10.58+
Form of Non-employee Director Option Agreement for the 2004 Plan (incorporated by reference from Exhibit 99.2 to the Company’s Current Report on Form 8-K filed with the Securities Exchange Commission on December 22, 2004).
   
10.59+
Form of Amendment to Form of Notice of Grant of Stock Option used under the Company’s 1995 Stock Option Plan (the “1995 Plan”) (incorporated by reference to Exhibit 10.5 to the quarterly Report on Form 10-Q for the quarter ended December 31, 2004).
 
 
   
10.60+
Form of Non-Employee Directors Stock Option Election Option Agreement used under the Company’s 1995 Plan (incorporated by reference to Exhibit 10.6 to the Quarterly Report on Form 10-Q for the quarter ended December 31, 2004).
   
10.61
First Amendment To Patent License Agreement entered into on or about July 1, 1991 by and between the Company and the University of Texas System, Austin (incorporated by reference to Exhibit 10.1 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2005).
   
10.64*
Assignment Agreement By and Between Pharmacyclics, Inc. and Applera Corporation dated April 7, 2006 (incorporated by reference to Exhibit 10.64 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2006).
   
10.65
Fourth Amendment to New Lease dated August 14, 2006 by and between the Company and Metropolitan Life Insurance Company (incorporated by reference to Exhibit 10.5 to the Company’s Current Report on Form 8-K filed with the Securities and Exchange Commission on August 17, 2006).
   
10.67
Fifth Amendment to New Lease dated July 11, 2008 by and between the Registrant and Metropolitan Life Insurance Company (incorporated by reference to Exhibit 10.6 to the Company’s Current Report on Form 8-K filed with the Securities and Exchange Commission on July 15, 2008).
   
10.68*
Amendment No. 1 to Assignment Agreement by and between Pharmacyclics, Inc. and Applera Corporation dated May 12, 2008 (incorporated by reference to Exhibit 10.68 to the Company’s Annual Report on Form 10-K for the year ended June 30, 2008).
   
10.69+
Form of Severance Agreement between the Company and certain executive officers (incorporated by reference to Exhibit 10.69 to the Company’s Annual Report on Form 10-K for the year ended June 30,2008).
   
10.70+
Offer letter dated July 9, 2008 by and between the Company and James Lowder, M.D. (incorporated by reference to Exhibit 10.70 to the Company’s Annual Report on Form 10-K for the year ended June 30, 2008).
   
10.71+
Separation Agreement effective as of September 10, 2008 by and between Richard A. Miller, M.D. and Pharmacyclics, Inc. (incorporated by reference to Exhibit 10.1 to the Quarterly Report on Form 10-Q for the quarter ended September 30, 2008).
   
10.72+
Separation Agreement effective as of September 10, 2008 by and between Leiv Lea and Pharmacyclics, Inc. (incorporated by reference to Exhibit 10.2 to the Quarterly Report on Form 10-Q for the quarter ended September 30, 2008).
   
10.73+
Form of Restricted Stock Award Agreement for the 2004 Plan (incorporated by reference to Exhibit 10.3 to the Quarterly Report on Form 10-Q for the quarter ended September 30, 2008).
   
10.74+
Offer letter dated April 13, 2006 by and between the Company and David J. Loury, Ph.D. (incorporated by reference to Exhibit 10.2 of the Registrant’s Current Report on Form 8-K filed with the Securities and Exchange Commission on November 13, 2008).
   
10.75+
Severance benefit agreement dated November 5, 2008 by and between the Company and David J. Loury, Ph.D. (incorporated by reference to Exhibit 10.1 of the Registrant’s Current Report on Form 8-K filed with the Securities and Exchange Commission on November 13, 2008).
 
 
   
10.76
Loan Agreement entered into between the Company and Robert W. Duggan & Associates dated as of December 30, 2008 (incorporated by reference to Exhibit 10.1 to the Quarterly Report on Form 10-Q for the quarter ended December 31, 2008).
   
10.77*
Amendment No. 2 to Assignment Agreement by and between Pharmacyclics, Inc. and Celera Corporation dated March 2, 2009 (incorporated by reference to Exhibit 10.1 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2009).
   
10.78*
Amendment No. 3 to Assignment Agreement by and between Pharmacyclics, inc. and Celera Corporation dated March 30, 2009 (incorporated by reference to Exhibit 10.2 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2009).
   
10.79
Amendment No. 1 to Loan Agreement entered into between the Company and Robert W. Duggan & Associates dated as of March 30, 2009 (incorporated by reference to Exhibit 10.3 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2009).
   
10.80+
Offer letter dated February 2, 2009 by and between the Company and Glenn C. Rice, Ph.D. (incorporated by reference to Exhibit 10.4 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2009).
   
10.81+
Offer letter dated February 5, 2009 by and between the Company and Rainer M. Erdtmann (incorporated by reference to Exhibit 10.5 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2009).
   
10.82+
Offer letter dated February 26, 2009 by and between the Company and Ahmed Hamdy, M.B.B.Ch. (incorporated by reference to Exhibit 10.6 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2009).
   
10.83**
Collaboration Agreement by and between Pharmacyclics, Inc. and Les Laboratoires Servier and Institut de Recherches Internationales Servier dated April 9, 2009 (filed with initial filing of Annual Report on Form 10-K for the year ended June 30, 2009).
   
10.84
Amendment No. 2 to Loan Agreement entered into between the Company and Robert W. Duggan and Blazon Corporation Profit Sharing Plan dated as of June 17, 2009 (filed with initial filing of Annual Report on Form 10-K for the year ended June 30, 2009).
   
23.1
Consent of Independent Registered Public Accounting Firm (filed with initial filing of Annual Report on Form 10-K for the year ended June 30, 2009).
   
24.1
Power of Attorney (filed with initial filing of Annual Report on Form 10-K for the year ended June 30, 2009).
   
31.1
Section 302 Certification of Chief Executive Officer.
   
31.2
Section 302 Certification of Principal Financial Officer.
   
32.1
Section 906 Certification of Chief Executive Officer and Principal Financial Officer.
 
_______________
 
*
Confidential treatment has been granted as to certain portions of this agreement.
+
Indicates a management contract or compensatory plan or arrangement.
**
Confidential treatment has been requested as to certain portions of this agreement.
 
 
SIGNATURES
 
Pursuant to the requirements of Section 13 or 15(d) of the Exchange Act, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized, on October 27, 2009.
 
PHARMACYCLICS, INC.
   
   
By:
 /s/ Robert W. Duggan
 
Name:
Robert W. Duggan
 
Title:
Chairman of the Board and Chief Executive Officer

Pursuant to the requirements of the Exchange Act, this report has been signed below by the following persons on behalf of the registrant and in the capacities indicated on the 27th day of October 2009.
 
By:
 /s/ Robert W. Duggan  
October 27, 2009
 
Robert W. Duggan, Chairman of the Board and Chief Executive Officer (Principal Executive Officer)
    
       
By:
*
  
October 27, 2009
 
Glenn C. Rice, Ph.D., President, Chief Operating Officer and Director
    
       
By:
 /s/ Rainer M. Erdtmann  
October 27, 2009
 
Rainer M. Erdtmann, Vice President, Finance and Administration and Secretary (Principal Financial and Accounting Officer)
    
       
By:
*
  
October 27, 2009
 
Jason T. Adelman, Director
    
       
By:
*
  
October 27, 2009
 
Cynthia C. Bamdad, Ph.D.
    
       
By:
*
  
October 27, 2009
 
David D. Smith, Ph.D.
    
       
By:
*
  
October 27, 2009
 
Minesh P. Mehta, M.D., Director
    
       
*By
 /s/ Rainer M. Erdtmann    
 
Rainer M. Erdtmann, Attorney-in-fact
    
 
 
 
Index to Exhibits and Financial Statement Schedules
 
Exhibit Number
Description
   
3.1
Amended and Restated Certificate of Incorporation of the Company (incorporated by reference to Exhibit 3.1 to the Company’s Current Report on Form 8-K filed with the Securities and Exchange Commission on December 16, 2008).
   
3.2
Amended and Restated Bylaws of the Company (incorporated by reference to Exhibit of the same number to the Quarterly Report on Form 10-Q for the quarter ended December 31, 2001).
   
3.3
Amendment to the Amended and Restated Bylaws of the Company (incorporated by reference to Exhibit 3.1 to the Periodic Report on Form 8-K filed on August 9, 2006).
   
4.2
Specimen Certificate of the Company’s Common Stock (incorporated by reference to Exhibit 4.2 to the Company’s Registration Statement on Form S-1, Commission File No. 33-96048).
   
4.3*
Stock Purchase Agreement By and Between Pharmacyclics, Inc. and Applera Corporation dated April 7, 2006 (incorporated by reference to Exhibit 4.3 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2006).
   
4.5
Form of Stock Purchase Agreement related to the February 19, 2009 sale of approximately 1.5 million shares of the Company’s common stock to certain foreign and U.S. individuals and entities of which some are shareholders of Pacific Biopharma Group, Ltd. (incorporated by reference to Exhibit 4.1 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2009).
   
10.6*
Patent License Agreement entered into between the Company and The University of Texas, Austin entered into on or about July 1, 1991 (incorporated by reference to Exhibit 10.8 to the Company’s Registration Statement on Form S-1, Commission File No. 33-96048).
   
10.7*
Patent License Agreement entered into between the Company and The University of Texas, Dallas dated as of July 1, 1992, as amended by the Patent License Agreement dated May 27, 1993 (incorporated by reference to Exhibit 10.9 to the Company’s Registration Statement on Form S-1, Commission File No. 33-96048).
   
10.8*
Patent License Agreement entered into between the Company and Stuart W. Young dated as of October 15, 1992 (incorporated by reference to Exhibit 10.10 to the Company’s Registration Statement on Form S-1, Commission File No. 33-96048).
   
10.9
Lease Agreement entered into between the Company and New England Mutual Life Insurance Company dated as of June 17, 1993, as amended on July 22, 1993, and as further amended on March 1, 1994 (incorporated by reference to Exhibit 10.11 to the Company’s Registration Statement on Form S-1, Commission File No. 33-96048).
   
10.13+
The Company’s 1995 Stock Option Plan (incorporated by reference to Exhibit 99.1 to the Company’s Registration Statement on Form S-8, Commission File No. 333-52881).
   
10.14+
The Company’s 1995 Non-Employee Directors’ Stock Option Plan (incorporated by reference to Exhibit 99.7 to the Company’s Registration Statement on Form S-8, Commission File No. 33-98514).
   
10.15+
The Company’s Employee Stock Purchase Plan as amended on October 9, 2008 (incorporated by reference to Exhibit 10.2 to the Company’s Current Report on Form 8-K filed with the Securities and Exchange Commission on December 16, 2008).
 
 
   
10.16+
Employment Agreement entered into between the Company and Richard A. Miller, M.D. dated as of June 10, 1992 (incorporated by reference to Exhibit 10.19 to the Company’s Registration Statement on Form S-1, Commission File No. 33-96048).
   
10.22+
Form of Notice of Grant of Stock Option generally to be used under the 1995 Stock Option Plan (incorporated by reference to Exhibit 99.2 to the Company’s Registration Statement on Form S-8, Commission File No. 33- 98514).
   
10.23+
Form of Stock Option Agreement (incorporated by reference to Exhibit 99.3 to the Company’s Registration Statement on Form S-8, Commission File No. 333-52881).
   
10.25+
Form of Addendum to Stock Option Agreement (Special Tax Election) (incorporated by reference to Exhibit 99.5 to the Company’s Registration Statement on Form S-8, Commission File No. 33-98514).
   
10.26+
Form of Addendum to Stock Option Agreement (Involuntary Termination following Change in Control) (incorporated by reference to Exhibit 99.6 to the Company’s Registration Statement on Form S-8, Commission File No. 33- 98514).
   
10.27+
Form of Notice of Grant of Automatic Stock Option (Initial Grant) (incorporated by reference to Exhibit 99.8 to the Company’s Registration Statement on Form S-8, Commission File No. 33-98514).
   
10.28+
Form of Notice of Grant of Automatic Stock Option (Annual Grant) (incorporated by reference to Exhibit 99.9 to the Company’s Registration Statement on Form S-8, Commission File No. 33-98514).
   
10.29+
Form of Non-Employee Director Stock Option Agreement (incorporated by reference to Exhibit 99.10 to the Company’s Registration Statement on Form S-8, Commission File No. 33-98514).
   
10.30+
Form of Employee Stock Purchase Plan Enrollment/Change Form (incorporated by reference to Exhibit 99.12 to the Company’s Registration Statement on Form S-8, Commission File No. 33-98514).
   
10.31+
Form of Stock Purchase Agreement (incorporated by reference to Exhibit 99.13 to the Company’s Registration Statement on Form S-8, Commission File No. 33-98514).
   
10.38+
Employment Agreement, dated December 18, 1997, by and between the Company and Leiv Lea (incorporated by reference to Exhibit 10.38 to the Quarterly report on Form 10-Q for the quarter ended March 31, 1998).
   
10.44*
Master Development and Supply Agreement, dated March 20, 2000 by and between Cook Imaging Corporation, D.B.A. Cook Pharmaceutical Solutions, and the Registrant (incorporated by reference to Exhibit 10.1 to the Quarterly report on Form 10-Q for the quarter ended March 31, 2000).
   
10.47*
Supply Agreement, dated December 11, 2000 by and between Dixie Chemical Company and the Registrant (incorporated by reference to Exhibit 10.1 to the Quarterly Report on Form 10-Q for the quarter ended December 31, 2000).
   
10.48*
Supply Agreement, dated December 18, 2000 by and between Lonza, AG and the Registrant (incorporated by reference to Exhibit 10.2 to the Quarterly Report on Form 10-Q for the quarter ended December 31, 2000).
 
 
   
10.49
Lease and Lease Termination Agreement dated June 14, 2000 by and between the Registrant and Metropolitan Life Insurance Company (incorporated by reference to Exhibit 10.49 to the Annual Report on Form 10-K for the year ended June 30, 2001).
   
10.50
First Amendment to New Lease dated April 10, 2001 by and between the Registrant and Metropolitan Life Insurance Company (incorporated by reference to Exhibit 10.50 to the Annual Report on Form 10-K for the year ended June 30, 2001).
   
10.51
Second Amendment to New Lease dated June 29, 2001 by and between the Registrant and Metropolitan Life Insurance Company (incorporated by reference to Exhibit 10.51 to the Annual Report on Form 10-K for the year ended June 30, 2001).
   
10.53*
Supply Agreement, dated August 17, 2001 by and between EMS-Dottikon AG and the Registrant (incorporated by reference to Exhibit 10.1 to the Quarterly Report on Form 10-Q for the quarter ended September 30, 2001).
   
10.54
Third Amendment to New Lease dated February 5, 2003 by and between the Registrant and Metropolitan Life Insurance Company (incorporated by reference to Exhibit 10.1 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2003).
   
10.55
Form of Indemnification Agreement between the Company and its directors and executive officers (incorporated by reference to Exhibit 10.55 to the Annual Report on Form 10-K for the year ended June 30, 2004).
   
10.56+
The Company’s 2004 Equity Incentive Award Plan (the “2004 Plan”) as amended on October 9, 2008 (incorporated by reference to Exhibit 10.1 to the Company’s Current Report on Form 8-K filed with the Securities and Exchange Commission on December 16, 2008).
   
10.57+
Form of Option Agreement for the 2004 Plan (incorporated by reference from Exhibit 99.1 to the Company’s Current Report on Form 8-K filed with the Securities and Exchange Commission on December 22, 2004).
   
10.58+
Form of Non-employee Director Option Agreement for the 2004 Plan (incorporated by reference from Exhibit 99.2 to the Company’s Current Report on Form 8-K filed with the Securities Exchange Commission on December 22, 2004).
   
10.59+
Form of Amendment to Form of Notice of Grant of Stock Option used under the Company’s 1995 Stock Option Plan (the “1995 Plan”) (incorporated by reference to Exhibit 10.5 to the quarterly Report on Form 10-Q for the quarter ended December 31, 2004).
   
10.60+
Form of Non-Employee Directors Stock Option Election Option Agreement used under the Company’s 1995 Plan (incorporated by reference to Exhibit 10.6 to the Quarterly Report on Form 10-Q for the quarter ended December 31, 2004).
   
10.61
First Amendment To Patent License Agreement entered into on or about July 1, 1991 by and between the Company and the University of Texas System, Austin (incorporated by reference to Exhibit 10.1 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2005).
   
10.64*
Assignment Agreement By and Between Pharmacyclics, Inc. and Applera Corporation dated April 7, 2006 (incorporated by reference to Exhibit 10.64 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2006).
   
10.65
Fourth Amendment to New Lease dated August 14, 2006 by and between the Company and Metropolitan Life Insurance Company (incorporated by reference to Exhibit 10.5 to the Company’s Current Report on Form 8-K filed with the Securities and Exchange Commission on August 17, 2006).
 
 
   
10.67
Fifth Amendment to New Lease dated July 11, 2008 by and between the Registrant and Metropolitan Life Insurance Company (incorporated by reference to Exhibit 10.6 to the Company’s Current Report on Form 8-K filed with the Securities and Exchange Commission on July 15, 2008).
   
10.68*
Amendment No. 1 to Assignment Agreement by and between Pharmacyclics, Inc. and Applera Corporation dated May 12, 2008 (incorporated by reference to Exhibit 10.68 to the Company’s Annual Report on Form 10-K for the year ended June 30, 2008).
   
10.69+
Form of Severance Agreement between the Company and certain executive officers (incorporated by reference to Exhibit 10.69 to the Company’s Annual Report on Form 10-K for the year ended June 30,2008).
   
10.70+
Offer letter dated July 9, 2008 by and between the Company and James Lowder, M.D. (incorporated by reference to Exhibit 10.70 to the Company’s Annual Report on Form 10-K for the year ended June 30, 2008).
   
10.71+
Separation Agreement effective as of September 10, 2008 by and between Richard A. Miller, M.D. and Pharmacyclics, Inc. (incorporated by reference to Exhibit 10.1 to the Quarterly Report on Form 10-Q for the quarter ended September 30, 2008).
   
10.72+
Separation Agreement effective as of September 10, 2008 by and between Leiv Lea and Pharmacyclics, Inc. (incorporated by reference to Exhibit 10.2 to the Quarterly Report on Form 10-Q for the quarter ended September 30, 2008).
   
10.73+
Form of Restricted Stock Award Agreement for the 2004 Plan (incorporated by reference to Exhibit 10.3 to the Quarterly Report on Form 10-Q for the quarter ended September 30, 2008).
   
10.74+
Offer letter dated April 13, 2006 by and between the Company and David J. Loury, Ph.D. (incorporated by reference to Exhibit 10.2 of the Registrant’s Current Report on Form 8-K filed with the Securities and Exchange Commission on November 13, 2008).
   
10.75+
Severance benefit agreement dated November 5, 2008 by and between the Company and David J. Loury, Ph.D. (incorporated by reference to Exhibit 10.1 of the Registrant’s Current Report on Form 8-K filed with the Securities and Exchange Commission on November 13, 2008).
   
10.76
Loan Agreement entered into between the Company and Robert W. Duggan & Associates dated as of December 30, 2008 (incorporated by reference to Exhibit 10.1 to the Quarterly Report on Form 10-Q for the quarter ended December 31, 2008).
   
10.77*
Amendment No. 2 to Assignment Agreement by and between Pharmacyclics, Inc. and Celera Corporation dated March 2, 2009 (incorporated by reference to Exhibit 10.1 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2009).
   
10.78*
Amendment No. 3 to Assignment Agreement by and between Pharmacyclics, inc. and Celera Corporation dated March 30, 2009 (incorporated by reference to Exhibit 10.2 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2009).
   
10.79
Amendment No. 1 to Loan Agreement entered into between the Company and Robert W. Duggan & Associates dated as of March 30, 2009 (incorporated by reference to Exhibit 10.3 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2009).
   
10.80+
Offer letter dated February 2, 2009 by and between the Company and Glenn C. Rice, Ph.D. (incorporated by reference to Exhibit 10.4 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2009).
 
 
   
10.81+
Offer letter dated February 5, 2009 by and between the Company and Rainer M. Erdtmann (incorporated by reference to Exhibit 10.5 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2009).
   
10.82+
Offer letter dated February 26, 2009 by and between the Company and Ahmed Hamdy, M.B.B.Ch. (incorporated by reference to Exhibit 10.6 to the Quarterly Report on Form 10-Q for the quarter ended March 31, 2009).
   
10.83**
Collaboration Agreement by and between Pharmacyclics, Inc. and Les Laboratoires Servier and Institut de Recherches Internationales Servier dated April 9, 2009 (filed with initial filing of Annual Report on Form 10-K for the year ended June 30, 2009).
   
10.84
Amendment No. 2 to Loan Agreement entered into between the Company and Robert W. Duggan and Blazon Corporation Profit Sharing Plan dated as of June 17, 2009 (filed with initial filing of Annual Report on Form 10-K for the year ended June 30, 2009).
   
23.1
Consent of Independent Registered Public Accounting Firm (filed with initial filing of Annual Report on Form 10-K for the year ended June 30, 2009).
   
24.1
Power of Attorney (filed with initial filing of Annual Report on Form 10-K for the year ended June 30, 2009).
   
31.1
Section 302 Certification of Chief Executive Officer.
   
31.2
Section 302 Certification of Principal Financial Officer.
   
32.1
Section 906 Certification of Chief Executive Officer and Principal Financial Officer.
 
_______________
 
*
Confidential treatment has been granted as to certain portions of this agreement.
+
Indicates a management contract or compensatory plan or arrangement.
**
Confidential treatment has been requested as to certain portions of this agreement.