| x | ANNUAL REPORT PURSUANT TO      SECTION 13 OR 15(d) OF THESECURITIES |
|---|---------------------------------------------------------------------|

|   | EXCHANGE      ACT OF 1934 |
|--------|---------------------------|

|  ̈ | TRANSITION REPORT PURSUANT TO      SECTION 13 OR 15(d) OF THE |
|--------|---------------------------------------------------------------|

|   | SECURITIES      EXCHANGE ACT OF 1934 |
|--------|--------------------------------------|

| 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 |

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

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

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PHARMACYCLICS

| PART III |                                                                                                | 1      |
|----------|-----------------------------------------------------------------------------------------------------|--------|
|     |                                                                                                |   |
| Item 10. | Directors, Executive Officers and Corporate      Governance                                         | 1      |
| Item 11. | Executive Compensation                                                                              | 4      |
| Item 12. | Security Ownership of Certain Beneficial Owners and      Management and Related Stockholder Matters | 11     |
| Item 13. | Certain Relationships and Related Transactions, and      Director Independence                      | 13     |
| Item 14. | Principal Accountant Fees and Services                                                              | 14     |
|     |                                                                                                |   |
| PART IV  |                                                                                                | 15     |
|     |                                                                                                |   |
| Item 15. | Exhibits and Financial Statement    Schedules                                                       | 15     |

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PARTIII

| Item 10. | Directors,      Executive Officers and CorporateGovernance |
|----------|------------------------------------------------------------|

| 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. |
|-----|-------------------------------------------------------------------------------------|

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| 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 Administrationand      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. |
|-----|-------------------------------------------------------------------------------------|

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| Item 11. | Executive      Compensation |
|----------|-----------------------------|

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|                                      |   |   |   |                                                                                  |   | 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. |
|-----|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

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|                         |   | 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. |
|-----|--------------------------------|

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|                          |   | 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 fiscal2010): |
|-----|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

|   Current      Directors: |   |  Fees      Forgone |   |   | Option      SharesReceived      in LieuOf      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: |
|-----|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

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| Current      Directors:        | GrantDate |   | GrantDateFair      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 |   |

| (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. |
|-----|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

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| Item 12. | Security      Ownership of Certain Beneficial Owners and Management and Related      Stockholder Matters |
|----------|----------------------------------------------------------------------------------------------------------|

|                                                          |   |                      |      |   |                      |   |   | 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 |   |

|   | · | 2004      Equity Incentive Award Plan |
|--------|--------|---------------------------------------|

|   | · | 1995      Stock Option Plan |
|--------|--------|-----------------------------|

|   | · | 1995      Non-Employee Director Stock OptionPlan |
|--------|--------|--------------------------------------------------|

|   | · | Employee      Stock Purchase Plan |
|--------|--------|-----------------------------------|

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|                                               |   | 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 | % |

| (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. |
|-----|-------------------------------------------|

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Table of Contents

| Item 13. | Certain      Relationships and Related Transactions, and Director      Independence |
|----------|-------------------------------------------------------------------------------------|

|                             |   |     |   |      |   |         |   | 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 |
|-----|-----------------------------------|

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Table of Contents

| Item 14. | Principal      Accountant Fees and Services |
|----------|---------------------------------------------|

|                    |   | 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 |   |

----

Table of Contents

PART 

| Item 15. | 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).                                                                                                                                                    |

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Table of Contents

|   |                                                                                                                                                                                                                                                                                                                                                          |
|--------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 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).                                                                                                                                                                         |

----

Table of Contents

|   |                                                                                                                                                                                                                                                                                                        |
|--------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 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).              |

----

Table of Contents

|   |                                                                                                                                                                                                                                                                                                           |
|--------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 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).            |

----

Table of Contents

|    |                                                                                                                                                                                                                                                                           |
|---------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 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. |
|----|-----------------------------------------------------------------------------------------------|

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Table of Contents

| PHARMACYCLICS,      INC. |
|--------------------------|
|                     |   |
|                     |   |
| By:                      | /s/      Robert      W. Duggan |
|                     | Name: | Robert      W. Duggan |
|                     | Title: | Chairman      of the Board and Chief ExecutiveOfficer |

| 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                                                                                           |   |                  |

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Table of Contents

| 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).                                                                                                                                                |

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Table of Contents

|   |                                                                                                                                                                                                                                                                                                        |
|--------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 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).                                                                           |

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Table of Contents

|   |                                                                                                                                                                                                                                                                                                            |
|--------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 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). |

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Table of Contents

|   |                                                                                                                                                                                                                                                                                                         |
|--------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 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).                                                                               |

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Table of Contents

|    |                                                                                                                                                                                                                                                                           |
|---------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 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. |
|----|-----------------------------------------------------------------------------------------------|