| ý | ANNUAL REPORT UNDER SECTION 13 OR 15 (d) OF THE SECURITIES EXCHANGE ACT OF 1934 |
|--------|---------------------------------------------------------------------------------|

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

| Commission File Number 000-26658 |
|----------------------------------|

| Pharmacyclics, Inc. |
|---------------------|

| (Exact name of Registrant as specified in its charter) |
|--------------------------------------------------------|

| Delaware                                                         |   | 94-3148201                        |
|------------------------------------------------------------------|--------|-----------------------------------|
| (State of or other jurisdiction ofIncorporation or organization) |   | (IRS Employer Identification No.) |

| 995 E. Arques Avenue Sunnyvale, CA       |   | 94085-4521 |
|------------------------------------------|--------|------------|
| (Address of principal executive offices) |   | (Zip code) |

|   | Registrant’s telephone number, including area code: (408) 774-0330 |   |
|--------|--------------------------------------------------------------------------|--------|

| Securities registered pursuant to Section 12(b) of the Act:                 |                  |
|----------------------------------------------------------------------------------|-----------------------|
|                                                                             | Name of Each Exchange |
| Title of Each Class                                                              | on Which Registered   |
| Common Stock, $0.0001 par value                                                  | Nasdaq Capital Market |
|                                                                             |                  |
| Securities registered pursuant to Section 12(g) of the Act:  None |                  |

| Large accelerated filer                                            |  ̈ | Accelerated filer         | ý |
|--------------------------------------------------------------------|--------|---------------------------|--------|
|                                                               |   |                      |   |
| Non-accelerated filer(Do not check if a smaller reporting company) |  ̈ | Smaller reporting company |  ̈ |

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| PART III                  |                                                                                           | PAGE   |
|---------------------------|------------------------------------------------------------------------------------------------|--------|
|                      |                                                                                           |   |
| Item 10.                  | Directors, Executive Officers and Corporate Governance                                         | 2      |
| Item 11.                  | Executive Compensation                                                                         | 8      |
| Item 12.                  | Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters | 22     |
| Item 13.                  | Certain Relationships and Related Transactions, and Director Independence                      | 24     |
| Item 14.                  | Principal Accountant Fees and Services                                                         | 26     |
|                      |                                                                                           |   |
| PART IV    |                                                                                           |   |
|                      |                                                                                           |   |
| Item 15.                  | Exhibits and Financial Statement Schedules                                                     | 27     |

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| Item 10.Directors, Executive Officers and Corporate Governance |
|----------------------------------------------------------------|

| Name                     |   | Age |   | Position(s) with the Company |   | Director Since |
|--------------------------|--------|-----|--------|------------------------------|--------|----------------|
| Robert W. Duggan         |   | 67  |   | Director, Chairman and CEO   |   |           | 2007 |   |
| Minesh P. Mehta, M.D.    |   | 53  |   | Director                     |   |           | 2008 |   |
| David D. Smith, Ph.D.    |   | 41  |   | Director                     |   |           | 2008 |   |
| Richard A. van den Broek |   | 45  |   | Director                     |   |           | 2009 |   |
| Robert F. Booth, Ph.D.   |   | 57  |   | Director                     |   |           | 2010 |   |
| Roy C. Hardiman          |   | 51  |   | Director                     |   |           | 2010 |   |
| Gwen A. Fyfe, M.D.       |   | 59  |   | Director                     |   |           | 2010 |   |

----

----

----

| Name                         |   | Age |   | Position                                                  |
|------------------------------|--------|-----|--------|-----------------------------------------------------------|
| Robert W. Duggan             |   | 67  |   | Chairman, Chief Executive Officer and Director            |
| Mahkam Zanganeh, D.D.S., MBA |   | 41  |   | Chief of Staff & Vice President, Business Development |
| David J. Loury, Ph.D.        |   | 55  |   | Chief Scientific Officer                                  |
| Rainer M. Erdtmann           |   | 48  |   | Vice President, Finance and Administration and Secretary  |
| Joseph J. Buggy, Ph.D.       |   | 44  |   | Vice President, Research                                  |
| Eric E. Hedrick, M.D.        |   | 46  |   | Vice President, Oncology Development                      |
| Gregory W. Hemmi, Ph.D.      |   | 46  |   | Vice President, Chemical Operations                       |
| Mark A. Asbury               |   | 48  |   | Vice President and General Counsel                        |

----

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----

----

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| Name and Principal Position                                                             |   | Fiscal Year |   | Salary(1)($) |   | Bonus($) |   | Option Awards(2)($) |   | All Other Compensation ($) |    | Total ($) |
|-----------------------------------------------------------------------------------------|--------|-------------|--------|--------------|--------|----------|--------|---------------------|--------|----------------------------|---------|-----------|
| Robert W. Duggan,  Chairman and Chief Executive Officer (3)                   |   | 2011        |   | -            |   | -        |   | -                   |   |                       | -       |      |   | - |
|                                                                                    |   | 2010        |   | -            |   | -        |   | -                   |   |                       | -       |      |   | - |
|                                                                                    |   | 2009        |   | -            |   | -        |   | -                   |   |                       | -       |      |   | - |
| Mahkam Zanganeh, D.D.S., MBA, Chief of Staff & Vice President, Business Development |   | 2011        |   | 267,422      |   | -        |   | 721,310             | (4)    |                       | 36,500  | (5)       |   | 1,025,232 |
| David J. Loury, Ph.D., Chief Scientific Officer                                         |   | 2011        |   | 326,300      |   | -        |   | 455,880             | (4)    |                       | 1,500   | (6)       |   | 783,680 |
|                                                                                    |   | 2010        |   | 305,481      |   | 5,900    |   | 400,775             | (4)    |                       | 1,500   | (6)       |   | 713,656 |
|                                                                                    |   | 2009        |   | 265,215      |   | -        |   | 199,095             |   |                       | 1,500   | (6)       |   | 465,810 |
| Rainer M. Erdtmann, Vice President, Finance and Administration                          |   | 2011        |   | 229,430      |   | -        |   | 530,303             | (4)    |                       | 1,500   | (6)       |   | 761,233 |
| Eric E. Hedrick, M.D., Vice President, Oncology Development                             |   | 2011        |   | 289,386      |   | -        |   | 240,531             |   |                       | 103,600 | (7)       |   | 633,517 |
| Ahmed Hamdy, M.D., Chief Medical Officer                                                |   | 2011        |   | 330,574      |   | -        |   | 639,336             | (4)    |                       | 59,000  | (8)       |   | 1,028,910 |
|                                                                                    |   | 2010        |   | 315,000      |   | 4,822    |   | 548,100             | (4)    |                       | -       |      |   | 867,922 |
|                                                                                    |   | 2009        |   | 83,596       |   | 25,000   |   | 39,833              |   |                       | -       |      |   | 148,429 |

| (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. The amounts set forth under this column represent the aggregate grant date fair value of stock options granted in each fiscal year for financial reporting purposes under Statement of Financial Accounting Standards ASC Topic 718, “Stock Compensation,” disregarding the estimate of forfeitures. The Company’s methodology, including its underlying estimates and assumptions used in calculating these values, is set forth in Note 6 to its audited financial statements included in its annual report on Form 10-K filed with the Securities and Exchange Commission for the fiscal year ended June 30, 2011. |
|-----|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| (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) | The amount shown includes the portion of awards with performance-based vesting conditions for which the established performance conditions were established during the year.  The grant date fair value was calculated using the probable outcome of the established performance conditions which approximated the highest level of achievement. |
|-----|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| (5) | Consists of payments by the Company for Dr. Zanganeh’s local housing and related costs. |
|-----|-----------------------------------------------------------------------------------------------|

| (6) | Consists of the Company’s matching contribution under its 401(k) plan. |
|-----|------------------------------------------------------------------------------|

| (7) | Consists of $85,200 in Fiscal 2011 consulting fees paid prior to Dr. Hedrick’s employment by the Company and $18,400 paid for Dr. Hedrick’s local housing and related costs. |
|-----|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| (8) | In May 2011, we entered into a separation agreement with Dr. Hamdy.  Included in all other compensation is a severance payment of approximately $25,000 and a payment of accrued vacation of approximately $34,000. |
|-----|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

----

| Name                         |   | Grant Date |         | Date of Compensation Committee action to grant awards with performance conditions (1) |   | Estimated future payouts undernon-equity incentive plan awards |   | Estimated future payouts underequity incentive plan awards (2) |        | All other stock awards: number of shares of stock or units |      | All other option awards: number of securities underlying options |   | Exercise or base price of option awards ($) |   | Grant date fair value of stock and option awards(3) ($) |
|------------------------------|--------|------------|--------------|---------------------------------------------------------------------------------------|--------|----------------------------------------------------------------|--------|----------------------------------------------------------------|-------------|------------------------------------------------------------|-----------|------------------------------------------------------------------|--------|---------------------------------------------|--------|---------------------------------------------------------|
|                         |   |       | Threshold($) |                                                                                  |   | Target ($)                                                     |   |                                                           | Maximum ($) |                                                       | Threshold |                                                             |   | Target                                      |   | Maximum                                                 |   |   |   |   |
| Robert W. Duggan             |   |       |         |                                                                                  |   |                                                           | -      |                                                           |        |                                                       | -         |                                                             |   |                                        | -      |                                                    |   | - |   |   |   | - |   |   | - |   |   | - |   |   | - |   |   | - |   |   | - |
| Mahkam Zanganeh, D.D.S., MBA |   | 10/13/10   |         |                                                                                  |   |                                                           | -      |                                                           |        |                                                       | -         |                                                             |   |                                        | -      |                                                    |   | - |   |   |   | - |   |   | - |   |   | - |   |   | 30,000 |   |   | 7.69 |   |   | 171,261 |
|                         |   | 10/14/10   |         |                                                                                  |   |                                                           | -      |                                                           |        |                                                       | -         |                                                             |   |                                        | -      |                                                    |   | - |   |   |   | - |   |   | - |   |   | - |   |   | 10,000 |   |   | 7.48 |   |   | 55,556 |
|                         |   | 12/13/10   |         |                                                                                  |   |                                                           | -      |                                                           |        |                                                       | -         |                                                             |   |                                        | -      |                                                    |   | - |   |   |   | - |   |   | - |   |   | - |   |   | 25,000 |   |   | 5.81 |   |   | 108,618 |
|                         |   | 5/5/11     |         | 4/11/10                                                                               |   |                                                           | -      |                                                           |        |                                                       | -         |                                                             |   |                                        | -      |                                                    |   | - |   |   |   | 37,500 |   |   | 37,500 |   |   | - |   |   | - |   |   | 7.19 |   |   | 169,125 |
|                         |   | 5/5/11     |         | 3/3/09                                                                                |   |                                                           | -      |                                                           |        |                                                       | -         |                                                             |   |                                        | -      |                                                    |   | - |   |   |   | 37,500 |   |   | 37,500 |   |   | - |   |   | - |   |   | 0.75 |   |   | 216,750 |
| David J. Loury, Ph.D.        |   | 10/13/10   |         |                                                                                  |   |                                                           | -      |                                                           |        |                                                       | -         |                                                             |   |                                        | -      |                                                    |   | - |   |   |   | - |   |   | - |   |   | - |   |   | 30,000 |   |   | 7.69 |   |   | 171,261 |
|                         |   | 10/14/10   |         |                                                                                  |   |                                                           | -      |                                                           |        |                                                       | -         |                                                             |   |                                        | -      |                                                    |   | - |   |   |   | - |   |   | - |   |   | - |   |   | 10,000 |   |   | 7.48 |   |   | 55,556 |
|                         |   | 5/5/11     |         | 4/11/10                                                                               |   |                                                           | -      |                                                           |        |                                                       | -         |                                                             |   |                                        | -      |                                                    |   | - |   |   |   | 18,750 |   |   | 18,750 |   |   | - |   |   | - |   |   | 7.19 |   |   | 84,563 |
|                         |   | 5/5/11     |         | 3/3/09                                                                                |   |                                                           | -      |                                                           |        |                                                       | -         |                                                             |   |                                        | -      |                                                    |   | - |   |   |   | 25,000 |   |   | 25,000 |   |   | - |   |   | - |   |   | 0.75 |   |   | 144,500 |
| Rainer M. Erdtmann           |   | 10/13/10   |         |                                                                                  |   |                                                           | -      |                                                           |        |                                                       | -         |                                                             |   |                                        | -      |                                                    |   | - |   |   |   | - |   |   | - |   |   | - |   |   | 30,000 |   |   | 7.69 |   |   | 171,261 |
|                         |   | 10/14/10   |         |                                                                                  |   |                                                           | -      |                                                           |        |                                                       | -         |                                                             |   |                                        | -      |                                                    |   | - |   |   |   | - |   |   | - |   |   | - |   |   | 3,000 |   |   | 7.48 |   |   | 16,667 |
|                         |   | 5/5/11     |         | 4/11/10                                                                               |   |                                                           | -      |                                                           |        |                                                       | -         |                                                             |   |                                        | -      |                                                    |   | - |   |   |   | 12,500 |   |   | 12,500 |   |   | - |   |   | - |   |   | 7.19 |   |   | 56,375 |
|                         |   | 5/5/11     |         | 2/5/09                                                                                |   |                                                           | -      |                                                           |        |                                                       | -         |                                                             |   |                                        | -      |                                                    |   | - |   |   |   | 50,000 |   |   | 50,000 |   |   | - |   |   | - |   |   | 0.91 |   |   | 286,000 |
| Eric E. Hedrick, M.D.        |   | 10/13/10   |         |                                                                                  |   |                                                           | -      |                                                           |        |                                                       | -         |                                                             |   |                                        | -      |                                                    |   | - |   |   |   | - |   |   | - |   |   | - |   |   | 10,000 |   |   | 7.69 |   |   | 57,087 |
|                         |   | 6/14/11    |         |                                                                                  |   |                                                           | -      |                                                           |        |                                                       | -         |                                                             |   |                                        | -      |                                                    |   | - |   |   |   | - |   |   | - |   |   | - |   |   | 30,000 |   |   | 8.88 |   |   | 183,444 |
| Ahmed Hamdy, M.D. (4)        |   | 10/13/10   |         |                                                                                  |   |                                                           | -      |                                                           |        |                                                       | -         |                                                             |   |                                        | -      |                                                    |   | - |   |   |   | - |   |   | - |   |   | - |   |   | 30,000 |   |   | 7.69 |   |   | 171,261 |
|                         |   | 5/5/11     |         | 4/11/10                                                                               |   |                                                           | -      |                                                           |        |                                                       | -         |                                                             |   |                                        | -      |                                                    |   | - |   |   |   | 7,500 |   |   | 7,500 |   |   | - |   |   | - |   |   | 7.19 |   |   | 33,825 |
|                         |   | 5/5/11     |         | 3/10/09                                                                               |   |                                                           | -      |                                                           |        |                                                       | -         |                                                             |   |                                        | -      |                                                    |   | - |   |   |   | 75,000 |   |   | 75,000 |   |   | - |   |   | - |   |   | 0.73 |   |   | 434,250 |

| (1) | The exercise price for options with performance conditions is the closing market price of the Company’s common stock on the date the Compensation Committee took action to award the grant.  The grant date is the date annual performance conditions were established and communicated, at which time the options were considered granted under ASC 718. |
|-----|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| (2) | The amounts shown reflect estimated payouts of performance-based stock options for the third year of the four-year performance period beginning in 2009 and for the second year of the four-year performance period beginning in 2010. |
|-----|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| (3) | The Company’s share-based compensation program includes incentive and non-statutory stock options. The amounts set forth under this column represent the aggregate grant date fair value of stock options granted in each fiscal year for financial reporting purposes under Statement of Financial Accounting Standards ASC Topic 718, “Stock Compensation,” disregarding the estimate of forfeitures. The Company’s methodology, including its underlying estimates and assumptions used in calculating these values, is set forth in Note 6 to its audited financial statements included in its annual report on Form 10-K filed with the Securities and Exchange Commission for the fiscal year ended June 30, 2011. |
|-----|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| (4) | In May 2011, we entered into a separation agreement with Dr. Hamdy, upon which date Dr. Hamdy forfeited all of his outstanding and unvested stock options, including all but 5,000 of the options granted during the year ended June 30, 2011. |
|-----|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

----

|                         |   | Option Awards                                                     |
|------------------------------|--------|-------------------------------------------------------------------|
| Name                         |   | Number of securities underlying unexercised options - exercisable |   | Number of securities underlying unexercised options -unexercisable |   | Equity incentive plan awards: number of securities underlying unexercised unearned options |   | Option exercise price $ |   | Option expiration date |
| Robert W. Duggan             |   |                                                              | - |   |   |   | - |   |   |   | - |   |   |   | - |   |   | - |   |
| Mahkam Zanganeh, D.D.S., MBA |   |                                                              | 84,770 | (1) |   |   |   |   |   |   |   |   |   |   | 2.30 |   |   | 9/10/2018 |   |
|                         |   |                                                              | 55,000 | (2) |   |   |   |   |   |   | 75,000 |   |   |   | 0.75 |   |   | 3/3/2019 |   |
|                         |   |                                                              | 37,500 | (3) |   |   |   |   |   |   | 112,500 |   |   |   | 7.19 |   |   | 4/11/2020 |   |
|                         |   |                                                              | 10,000 | (4) |   |   |   |   |   |   |   |   |   |   | 6.75 |   |   | 6/2/2020 |   |
|                         |   |                                                              | 30,000 | (5) |   |   |   |   |   |   |   |   |   |   | 7.69 |   |   | 10/13/2020 |   |
|                         |   |                                                              | 10,000 | (6) |   |   |   |   |   |   |   |   |   |   | 7.48 |   |   | 10/14/2020 |   |
|                         |   |                                                              | 25,000 | (7) |   |   |   |   |   |   |   |   |   |   | 5.81 |   |   | 12/13/2020 |   |
| David J. Loury, Ph.D.        |   |                                                              | 65,000 | (8) |   |   |   |   |   |   |   |   |   |   | 4.16 |   |   | 5/23/2016 |   |
|                         |   |                                                              | 75,000 | (9) |   |   |   |   |   |   |   |   |   |   | 2.76 |   |   | 3/13/2017 |   |
|                         |   |                                                              | 125,000 | (10) |   |   |   |   |   |   |   |   |   |   | 0.86 |   |   | 3/18/2018 |   |
|                         |   |                                                              | 154,074 | (11) |   |   | 45,926 |   |   |   |   |   |   |   | 1.35 |   |   | 11/4/2018 |   |
|                         |   |                                                              | 50,000 | (2) |   |   |   |   |   |   | 50,000 |   |   |   | 0.75 |   |   | 3/3/2019 |   |
|                         |   |                                                              | 30,974 | (12) |   |   | 19,026 |   |   |   |   |   |   |   | 3.51 |   |   | 1/12/2020 |   |
|                         |   |                                                              | 18,750 | (3) |   |   |   |   |   |   | 56,250 |   |   |   | 7.19 |   |   | 4/11/2020 |   |
|                         |   |                                                              | 30,000 | (5) |   |   |   |   |   |   |   |   |   |   | 7.69 |   |   | 10/13/2020 |   |
|                         |   |                                                              | 10,000 | (6) |   |   |   |   |   |   |   |   |   |   | 7.48 |   |   | 10/14/2020 |   |
| Rainer M. Erdtmann           |   |                                                              | 200,000 | (13) |   |   |   |   |   |   | 100,000 |   |   |   | 0.91 |   |   | 2/5/2019 |   |
|                         |   |                                                              | 12,500 | (3) |   |   |   |   |   |   | 37,500 |   |   |   | 7.19 |   |   | 4/11/2020 |   |
|                         |   |                                                              | 28,684 | (5) |   |   | 1,316 |   |   |   |   |   |   |   | 7.69 |   |   | 10/13/2020 |   |
|                         |   |                                                              | 3,000 | (6) |   |   |   |   |   |   |   |   |   |   | 7.48 |   |   | 10/14/2020 |   |
| Eric E. Hedrick, M.D.        |   |                                                              | 250,000 | (14) |   |   |   |   |   |   |   |   |   |   | 6.56 |   |   | 6/4/2020 |   |
|                         |   |                                                              | 10,000 | (5) |   |   |   |   |   |   |   |   |   |   | 7.69 |   |   | 10/13/2020 |   |
|                         |   |                                                              | 11,261 | (15) |   |   | 18,739 |   |   |   |   |   |   |   | 8.88 |   |   | 6/14/2021 |   |
| Ahmed Hamdy, M.D.            |   |                                                              | - |   |   |   | - |   |   |   | - |   |   |   | - |   |   | - |   |

| (1) | Option vests in forty-eight (48) equal installments beginning on the date of grant (September 10, 2008). |
|-----|----------------------------------------------------------------------------------------------------------|

| (2) | 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. |
|-----|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| (3) | Option vests in four equal annual installments beginning April 11, 2011, subject to the satisfaction of certain performance criteria with respect to each annual period. |
|-----|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| (4) | Option vests in forty-eight (48) equal installments beginning on the date of grant (June 2, 1010). |
|-----|----------------------------------------------------------------------------------------------------|

| (5) | Option vests in forty-eight (48) equal installments beginning on the date of grant (October 13, 2010). |
|-----|--------------------------------------------------------------------------------------------------------|

| (6) | Option vests in forty-eight (48) equal installments beginning on the date of grant (October 14, 2010). |
|-----|--------------------------------------------------------------------------------------------------------|

| (7) | Option vests in forty-eight (48) equal installments beginning on the date of grant (December 13, 2010). |
|-----|---------------------------------------------------------------------------------------------------------|

----

| (8) | 25% of the shares subject to the option vest on the one year anniversary of the date of grant (May 23, 2006) and the remaining shares subject to the option vest in a series of 36 equal and successive monthly installments thereafter. |
|-----|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| (9) | Option vests in forty-eight (48) equal installments beginning on the date of grant (March 13, 2007). |
|-----|------------------------------------------------------------------------------------------------------|

| (10) | Option vests in forty-eight (48) equal installments beginning on the date of grant (March 18, 2008). |
|------|------------------------------------------------------------------------------------------------------|

| (11) | Option vests in a series of five equal and successive annual installments measured from November 4, 2008. |
|------|-----------------------------------------------------------------------------------------------------------|

| (12) | 25% of the shares subject to the option vest on the one year anniversary of the date of grant (January 12, 2010) and the remaining shares subject to the option vest in a series of 36 equal and successive monthly installments thereafter. |
|------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| (13) | Option vests in four equal annual installments beginning February 5, 2010, subject to the satisfaction of certain performance criteria with respect to each annual period. |
|------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| (14) | 15,625 option shares vested on August 24, 2010 and the remaining 234,375 option shares vest in a series of 45 equal and successive monthly installments from August 24, 2010. |
|------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| (15) | Option vests in forty-eight (48) equal installment beginning on the date of grant (June 14, 2011). |
|------|----------------------------------------------------------------------------------------------------|

| Name                         |                                  | Option Awards |
|------------------------------|---------------------------------------|---------------|
|                         | Number of shares acquired on exercise |          | Value realized on exercise (1) $ |
| Robert W. Duggan             |                                  | -             |   | - |
| Mahkam Zanganeh, D.D.S., MBA |                                  | 85,230        |   | 312,638 |
| David J. Loury, Ph.D.        |                                  | -             |   | - |
| Rainer M. Erdtmann           |                                  | -             |   | - |
| Eric E. Hedrick, M.D.        |                                  | -             |   | - |
| Ahmed Hamdy, M.D.            |                                  | 162,500       |   | 1,188,457 |

| (1) | Value realized on exercise is based on the fair market value of our common stock on the date of exercise minus the exercise price and does not necessarily reflect proceeds actually received by the named executive officer. |
|-----|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

----

----

| Current Directors:        |   | Fees Earned or Paid in Cash (1)($) |   |   | Option Awards (2)($) |   |    | Total($) |   |
|---------------------------|--------|------------------------------------|--------|--------|----------------------|--------|---------|----------|--------|
| Robert W. Duggan          |   |                               | -      |   |                 |   | -       |     |   |   | - |   |
| Robert F. Booth, Ph.D.    |   |                               | -      |   |                 |   | 161,044 |     |   |   | 161,044 |   |
| Roy C. Hardiman           |   |                               | -      |   |                 |   | 161,044 |     |   |   | 161,044 |   |
| Minesh P. Mehta, M.D.     |   |                               | 14,000 |   |                 |   | 62,061  |     |   |   | 76,061 |   |
| David D. Smith, Ph.D. (3) |   |                               | -      |   |                 |   | 101,969 |     |   |   | 101,969 |   |
| Richard A. van den Broek  |   |                               | -      |   |                 |   | 200,344 |     |   |   | 200,344 |   |
| Gwen A. Fyfe, M.D. (4)    |   |                               | -      |   |                 |   | 161,044 |     |   |   | 161,044 |   |
|                      |   |                               |   |   |                 |   |    |     |   |   |   |   |
| Former Directors:         |   |                               |   |   |                 |   |    |     |   |   |   |   |
| Jason T. Adelman          |   |                               | -      |   |                 |   | 49,524  |     |   |   | 49,524 |   |
| Cynthia C. Bamdad, Ph.D.  |   |                               | -      |   |                 |   | 36,604  |     |   |   | 36,604 |   |
| Glenn C. Rice, Ph.D.      |   |                               | -      |   |                 |   | 32,300  |     |   |   | 32,300 |   |

| (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, 2011.  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 2011 where the related options were granted the first day of fiscal 2012): |
|-----|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| Current Directors:       |   | Fees Forgone ($) |   |   | Option Shares Received in Lieu Of Cash |   |
|--------------------------|--------|------------------|--------|--------|----------------------------------------|--------|
| Robert W. Duggan         |   |             | -      |   |                                   |   | - |   |
| Robert F. Booth, Ph.D.   |   |             | 15,000 |   |                                   |   | 5,869 |   |
| Roy C. Hardiman          |   |             | 15,000 |   |                                   |   | 5,869 |   |
| Minesh P. Mehta, M.D.    |   |             | 14,000 |   |                                   |   | 5,267 |   |
| David D. Smith, Ph.D.    |   |             | 33,000 |   |                                   |   | 13,285 |   |
| Richard A. van den Broek |   |             | 38,500 |   |                                   |   | 15,495 |   |
| Gwen A. Fyfe, M.D.       |   |             | 15,000 |   |                                   |   | 5,869 |   |
|                     |   |             |   |   |                                   |   |   |   |
| Former Directors:        |   |             |   |   |                                   |   |   |   |
| Jason T. Adelman         |   |             | 23,000 |   |                                   |   | 9,537 |   |
| Cynthia C. Bamdad, Ph.D. |   |             | 17,000 |   |                                   |   | 7,049 |   |
| Glenn C. Rice, Ph.D.     |   |             | 15,000 |   |                                   |   | 6,220 |   |

| (2) | The amounts set forth under this column represent the aggregate grant date fair value of stock options granted in each fiscal year for financial reporting purposes under Statement of Financial Accounting Standards ASC Topic 718, “Stock Compensation,” disregarding the estimate of forfeitures. The Company’s methodology, including its underlying estimates and assumptions used in calculating these values, is set forth in Note 6 to its audited financial statements included in its annual report on Form 10-K filed with the Securities and Exchange Commission for the fiscal year ended June 30, 2011.  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, 2011. The grant date fair value of option awards granted in fiscal year 2011 and the total options outstanding are as follows: |
|-----|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

----

| Current Directors:       |   | Grant Date |   | Grant DateFair Value |    |   | Options Outstanding at 7/1/11 |   |
|--------------------------|--------|------------|--------|----------------------|---------|--------|-------------------------------|--------|
| Robert F. Booth, Ph.D.   |   | 12/9/10    |   | $                    | 43,075  |   |                          |   |   |
|                     |   | 12/13/10   |   |                 | 86,894  |   |                          |   |   |
|                     |   | 4/1/11     |   |                 | 15,563  |   |                          |   |   |
|                     |   | 7/1/11     |   |                 | 15,512  |   |                          |   |   |
|                     |   |       |   | $                    | 161,044 |   |                          |   | 35,869 |   |
| Roy C. Hardiman          |   | 12/9/10    |   | $                    | 43,075  |   |                          |   |   |   |
|                     |   | 12/13/10   |   |                 | 86,894  |   |                          |   |   |   |
|                     |   | 4/1/11     |   |                 | 15,563  |   |                          |   |   |   |
|                     |   | 7/1/11     |   |                 | 15,512  |   |                          |   |   |   |
|                     |   |       |   | $                    | 161,044 |   |                          |   | 35,869 |   |
| Minesh P. Mehta, M.D.    |   | 10/1/10    |   | $                    | 10,590  |   |                          |   |   |   |
|                     |   | 12/9/10    |   |                 | 32,306  |   |                          |   |   |   |
|                     |   | 1/3/11     |   |                 | 9,865   |   |                          |   |   |   |
|                     |   | 4/1/11     |   |                 | 516     |   |                          |   |   |   |
|                     |   | 7/1/11     |   |                 | 8,784   |   |                          |   |   |   |
|                     |   |       |   | $                    | 62,061  |   |                          |   | 44,407 |   |
| David D. Smith, Ph.D.    |   | 10/1/10    |   | $                    | 17,834  |   |                          |   |   |   |
|                     |   | 12/9/10    |   |                 | 32,306  |   |                          |   |   |   |
|                     |   | 1/3/11     |   |                 | 16,614  |   |                          |   |   |   |
|                     |   | 4/1/11     |   |                 | 17,637  |   |                          |   |   |   |
|                     |   | 7/1/11     |   |                 | 17,578  |   |                          |   |   |   |
|                     |   |       |   | $                    | 101,969 |   |                          |   | 156,986 |   |
| Richard A. van den Broek |   | 10/1/10    |   | $                    | 18,951  |   |                          |   |   |   |
|                     |   | 12/9/10    |   |                 | 32,306  |   |                          |   |   |   |
|                     |   | 12/13/10   |   |                 | 86,894  |   |                          |   |   |   |
|                     |   | 1/3/11     |   |                 | 18,691  |   |                          |   |   |   |
|                     |   | 4/1/11     |   |                 | 21,787  |   |                          |   |   |   |
|                     |   | 7/1/11     |   |                 | 21,715  |   |                          |   |   |   |
|                     |   |       |   | $                    | 200,344 |   |                          |   | 67,427 |   |
| Gwen A. Fyfe, M.D.       |   | 12/9/10    |   | $                    | 43,075  |   |                          |   |   |   |
|                     |   | 12/13/10   |   |                 | 86,894  |   |                          |   |   |   |
|                     |   | 4/1/11     |   |                 | 15,563  |   |                          |   |   |   |
|                     |   | 7/1/11     |   |                 | 15,512  |   |                          |   |   |   |
|                     |   |       |   | $                    | 161,044 |   |                          |   | 365,869 |   |

----

| Former Directors:        |    |   |   |   |   |   |   |
|--------------------------|---------|--------|--------|--------|--------|--------|--------|
| Jason T. Adelman         | 10/1/10 |   | $      | 25,641 |   |   |   |   |
|                     | 1/3/11  |   |   | 23,883 |   |   |   |   |
|                     |    |   | $      | 49,524 |   |   |   | 52,106 |   |
| Cynthia C. Bamdad, Ph.D. | 10/1/10 |   | $      | 18,951 |   |   |   |   |   |
|                     | 1/3/11  |   |   | 17,653 |   |   |   |   |   |
|                     |    |   | $      | 36,604 |   |   |   | 34,752 |   |
| Glenn C. Rice, Ph.D.     | 10/1/10 |   | $      | 16,724 |   |   |   |   |   |
|                     | 1/3/11  |   |   | 15,576 |   |   |   |   |   |
|                     |    |   | $      | 32,300 |   |   |   | 12,946 |   |

|   | There were no options that were repriced or otherwise materially modified during fiscal year 2011. |
|--------|----------------------------------------------------------------------------------------------------|

| (3) | Prior to his appointment to the Audit Committee or the Compensation Committee, Dr. Smith also was granted options in August 2010 to purchase 1,100 shares of the Company’s common stock, valued as of the grant date at less than $8,000, in connection with consulting services provided in fiscal 2010. |
|-----|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| (4) | Dr. Fyfe also provides consulting services to the Company under a Consulting Services Agreement that is cancelable by either party upon 30 days written notice.  Dr. Fyfe was paid $97,000 and $490,000 for consulting services provided during fiscal year 2010 and 2011, respectively and $89,000 for consulting services provided during the period from July 1, 2011 to September 30, 2011.  Additionally, Dr. Fyfe was granted options to purchase 300,000 shares and 30,000 shares of the Company’s common stock in connection with her consulting services during fiscal year 2010 and 2011, respectively, which vest monthly over a period of 48 months.  The grant date fair value of these option grants in fiscal 2010 and 2011 was $1,771,000 and $152,000, respectively. |
|-----|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

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

| Plan Category                                              |   | Number of securities to be issued upon exercise of outstanding options, warrants and rights(a) |      |   | Weighted-average exercise price of outstanding options, warrants and rights(b) |   |   | Number of securities remaining available for future issuance under equity compensation plans (excluding securities reflected in column (a))(c) (1) |   |
|------------------------------------------------------------|--------|------------------------------------------------------------------------------------------------|-----------|--------|--------------------------------------------------------------------------------|--------|--------|---------------------------------------------------------------------------------------------------------------------------------------------------------|--------|
| Equity compensation plans approved by security holders (2) |   |                                                                                           | 6,858,198 |   |                                                                           | $      | 4.78   |                                                                                                                                                    |   |   | 3,850,667 |   |
| Equity compensation plans not approved by security holders |   |                                                                                           | -         |   |                                                                           |   | -      |                                                                                                                                                    |   |   | - |   |
| Total                                                      |   |                                                                                           | 6,858,198 |   |                                                                           | $      | 4.78   |                                                                                                                                                    |   |   | 3,850,667 |   |

----

| (1) | Includes approximately 136,530 shares issuable under the Company’s Employee Stock Purchase Plan. |
|-----|--------------------------------------------------------------------------------------------------------|

| (2) | Includes our: |
|-----|---------------|

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

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

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

|                                                                                    |   | Beneficial Ownership (1)           |       |
|-----------------------------------------------------------------------------------------|--------|------------------------------------|------------|
| Name                                                                                    |   | Outstanding Shares of Common Stock |       |   | Shares Issuable Pursuant to Options Vested and Exercisable Within 60 Days ofOctober 14, 2011 |   |   | Percent of Total Shares Outstanding |   |
|                                                                                    |   |                               |       |   |   |   |   |   |   |
| Felix J. Baker and Julian C. Baker (2)                                                  |   |                               | 7,201,016  |   |   |   | - |   |   |   | 10.5 | % |
| 667 Madison Avenue                                                                      |   |                               |       |   |   |   |   |   |   |   |   |   |
| New York, NY  10065                                                           |   |                               |       |   |   |   |   |   |   |   |   |   |
| Samuel D. Isaly (3)                                                                     |   |                               | 5,313,500  |   |   |   | - |   |   |   | 7.7 | % |
| 767 Third Avenue, 30th Floor                                                            |   |                               |       |   |   |   |   |   |   |   |   |   |
| New York, NY  10017                                                           |   |                               |       |   |   |   |   |   |   |   |   |   |
| PRIMECAP Management Company(4)                                                          |   |                               | 4,011,958  |   |   |   | - |   |   |   | 5.9 | % |
| 225 South Lake Ave., #400                                                               |   |                               |       |   |   |   |   |   |   |   |   |   |
| Pasadena, CA 91101                                                                      |   |                               |       |   |   |   |   |   |   |   |   |   |
| Robert W. Duggan (5)                                                                    |   |                               | 14,016,492 |   |   |   | - |   |   |   | 20.4 | % |
| Robert F. Booth, Ph.D.                                                                  |   |                               | -          |   |   |   | 13,858 |   |   |   | * |   |
| Gwen A. Fyfe, M.D.                                                                      |   |                               | -          |   |   |   | 139,521 |   |   |   | * |   |
| Roy C. Hardiman                                                                         |   |                               | -          |   |   |   | 13,858 |   |   |   | * |   |
| Minesh P. Mehta, M.D.                                                                   |   |                               | -          |   |   |   | 41,533 |   |   |   | * |   |
| David D. Smith, Ph.D.                                                                   |   |                               | 2,000      |   |   |   | 155,903 |   |   |   | * |   |
| Richard A. van den Broek                                                                |   |                               | 138,730    |   |   |   | 46,211 |   |   |   | * |   |
| Rainer M. Erdtmann                                                                      |   |                               | 22,246     |   |   |   | 222,063 |   |   |   | * |   |
| Eric E. Hedrick, M.D.                                                                   |   |                               | 2,814      |   |   |   | 99,792 |   |   |   | * |   |
| David J. Loury, Ph.D.                                                                   |   |                               | 25,980     |   |   |   | 478,749 |   |   |   | * |   |
| Mahkam Zanganeh, D.D.S., MBA                                                            |   |                               | 303,344    |   |   |   | 170,603 |   |   |   | * |   |
| Ahmed Hamdy, M.D                                                                        |   |                               | 11,966     |   |   |   | - |   |   |   | * |   |
|                                                                                    |   |                               |       |   |   |   |   |   |   |   |   |   |
| All current executive officers, directors and director nominees as a group (14 persons) |   |                               | 14,534,685 |   |   |   | 2,012,961 |   |   |   | 23.4 | % |

| * Less than 1%. |
|-----------------|

----

| (1) | Beneficial ownership is determined in accordance with the rules of the SEC and generally includes voting or investment power with respect to securities. Beneficial ownership also includes shares of stock subject to options which are vested and exercisable within sixty (60) days of the October 14, 2011 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 68,572,152 shares of Common Stock outstanding as of October 14, 2011, 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 the Forms 4 filed October 4, 2011.  The shares are held by 14159 Capital (GP), LLC, which beneficially owns 152,654 shares, Baker Brothers Life Sciences Capital (GP), LLC, which beneficially owns 6,895,680 shares, and Baker Biotech Capital (GP), LLC, which beneficially owns 152,682 shares, for which Felix J. Baker and Julian C. Baker are controlling members.  Felix J. Baker and Julian C. Baker may each be deemed to be beneficial owners of the shares and may be deemed to have shared voting and dispositive power with respect to the shares. |
|-----|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| (3) | Derived from a Form 13G/A filed February 11, 2011.  The shares are held by OrbiMed Advisors LLC, which beneficially owns 1,528,500 shares, and OrbiMed Capital LLC, which beneficially owns 3,785,000 shares, for which Samuel D. Isaly is the Managing Member.  Mr. Isaly may be deemed to have shared voting and dispositive power with respect to the shares. |
|-----|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| (4) | Derived from a Form 13F-HR filed on August 12, 2011. |
|-----|------------------------------------------------------|

| (5) | Derived from a Form 4 filed June 24, 2011.  Mr. Duggan disclaims beneficial ownership of 524,114 shares held in managed accounts, except to the extent of his pecuniary interest in those shares. |
|-----|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

----

| Current Directors:       |   | Board    |   | AuditCommittee |   | Compensation Committee |   | Nominating and Corporate Governance Committee |
|--------------------------|--------|----------|--------|----------------|--------|------------------------|--------|-----------------------------------------------|
| Robert W. Duggan         |   | Chairman |   |           |   |                   |   |                                          |
| Minesh P. Mehta, M.D.    |   | Member   |   | Member         |   | Member                 |   |                                          |
| David D. Smith, Ph.D.    |   | Member   |   | Member         |   | Member                 |   | Member                                        |
| Richard A. van den Broek |   | Member   |   | Chairman       |   | Chairman               |   | Member                                        |
| Robert F. Booth, Ph.D.   |   | Member   |   |           |   |                   |   | Member                                        |
| Roy C. Hardiman          |   | Member   |   |           |   |                   |   | Chairman                                      |
| Gwen A. Fyfe, M.D.       |   | Member   |   |           |   |                   |   |                                          |

----

|               |   | Fiscal2011 |    |   | Fiscal2010 |   |
|--------------------|--------|------------|---------|--------|------------|--------|
| Audit fees         |   | $          | 368,300 |   |       | $      | 332,800 |   |
| Audit-related fees |   |       | -       |   |       |   | - |   |
| Tax fees           |   |       | 39,800  |   |       |   | 40,800 |   |
| All other fees     |   |       | -       |   |       |   | - |   |
| Total              |   | $          | 408,100 |   |       | $      | 373,600 |   |

----

----

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

|   | Signature                                  |   | Title                                                                       |   | Date             |
|--------|--------------------------------------------|--------|-----------------------------------------------------------------------------|--------|------------------|
|   |                                       |   |                                                                        |   |             |
|   | /s/ Robert W. Duggan                       |   | Chairman of the Board and                                                   |   | October 28, 2011 |
|   | Robert W. Duggan                           |   | Chief Executive Officer(Principal Executive Officer)                        |   |             |
|   |                                       |   |                                                                        |   |             |
|   | /s/ Rainer (Ramses) Erdtmann               |   | VP Finance and Administration                                               |   | October 28, 2011 |
|   | Rainer (Ramses) Erdtmann                   |   | and Secretary(Principal Financial Officer and Principal Accounting Officer) |   |             |
|   |                                       |   |                                                                        |   |             |
|   | *                                          |   | Director                                                                    |   | October 28, 2011 |
|   | Robert F. Booth, Ph.D.                     |   |                                                                        |   |             |
|   |                                       |   |                                                                        |   |             |
|   | *                                          |   | Director                                                                    |   | October 28, 2011 |
|   | Gwen A. Fyfe, M.D.                         |   |                                                                        |   |             |
|   |                                       |   |                                                                        |   |             |
|   | *                                          |   | Director                                                                    |   | October 28, 2011 |
|   | Roy C. Hardiman                            |   |                                                                        |   |             |
|   |                                       |   |                                                                        |   |             |
|   | *                                     |   | Director                                                                    |   | October 28, 2011 |
|   | David D. Smith, Ph.D.                      |   |                                                                        |   |             |
|   |                                       |   |                                                                        |   |             |
|   | *                                          |   | Director                                                                    |   | October 28, 2011 |
|   | Minesh P. Mehta, M.D.                      |   |                                                                        |   |             |
|   |                                       |   |                                                                        |   |             |
|   | *                                          |   | Director                                                                    |   | October 28, 2011 |
|   | Richard van den Broek                      |   |                                                                        |   |             |
|   |                                       |   |                                                                        |   |             |
| *By:   | /s/ Rainer (Ramses) Erdtmann               |   |                                                                        |   |             |
|   | Rainer (Ramses) Erdtmann, Attorney-in-fact |   |                                                                        |   |             |

----

| 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).                                                                                                                                                              |
| 3.4            | Amendment to the Amended and Restated Bylaws of the Company (filed with the initial filing of the Annual Report on Form 10-K for the year ended June 30, 2011).                                                                                                                                                                 |
| 4.1            | 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).                                                                                                                                                |
| 4.2*           | 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).                                                                                                   |
| 10.1*          | 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).                                                              |
| 10.2           | 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).  |
| 10.3+          | 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).                                                                                                                                                            |
| 10.4+          | 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).                                                                                  |
| 10.5+          | 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).                                                                                                    |

----

| 10.6+ | 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).                                                             |
|-------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 10.7+ | 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).                           |
| 10.8+ | 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). |

| 10.9+  | 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).                                                  |
|--------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 10.10+ | 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).                                                   |
| 10.11+ | 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).                                                       |
| 10.12+ | 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).                                                                                  |
| 10.13  | 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).  |
| 10.14  | 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).          |
| 10.15  | 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).          |
| 10.16  | 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).  |

----

| 10.17  | 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).                                                           |
|--------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 10.18+ | 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).      |
| 10.19+ | 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).                                                              |
| 10.20+ | 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).                                            |
| 10.21+ | 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).                  |
| 10.22  | 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). |

| 10.23* | 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).                                                               |
|--------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 10.24  | 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).      |
| 10.25  | 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).  |
| 10.26* | 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).                                    |

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| 10.27+ | 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).                                                                                                      |
|--------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 10.28+ | 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).                            |
| 10.29+ | 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).           |
| 10.30  | 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).                                              |
| 10.31* | 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).                                               |
| 10.32* | 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).                                              |
| 10.33  | 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).                                 |
| 10.34+ | 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).                                                                               |
| 10.35* | Collaboration Agreement by and between Pharmacyclics, Inc. and Les Laboratoires Servier and Institut de Recherches Internationales Servier dated April 9, 2009 (incorporated by reference to Exhibit 10.83 to the Company’s Annual Report on Form 10-K for the year ended June 30, 2009). |

| 10.36  | 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 (incorporated by reference to Exhibit 10.84 to the Company’s Annual Report on Form 10-K for the year ended June 30, 2009).  |
|--------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 10.37* | Drug Supply Agreement by and between Pharmacyclics, Inc. and Les Laboratoires Servier dated December 18, 2009 (incorporated by reference to Exhibit 10.1 to the Quarterly Report on Form 10-Q for the quarter ended December 31, 2009).                                                        |

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| 10.38 | Agreement and Release with Glenn Rice dated October 28, 2009 (incorporated by reference to Exhibit 10.2 to the Quarterly Report on Form 10-Q for the quarter ended December 31, 2009).                                                                                         |
|-------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 10.39 | Form of Stock Purchase Agreement by and between Pharmacyclics, Inc. and various institutional investors dated June 16, 2010 (incorporated by reference to Exhibit 10.1 to the Current Report on Form 8-K filed with the Securities and Exchange Commission on June 17, 2010).  |
| 10.40 | Sixth Amendment to New Lease dated January 20, 2011 by and between the Company 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, 2011).                                  |
| 10.41 | Form of Stock Purchase Agreement by and between the Company and various institutional investors dated June 17, 2011 (incorporated by reference to Exhibit 10.1 to the Current Report on Form 8-K filed with the Securities and Exchange Commission on June 17, 2011).          |
| 23.1  | Consent of Independent Registered Public Accounting Firm (filed with the initial filing of the Annual Report on Form 10-K for the year ended June 30, 2011).                                                                                                                   |
| 24.1  | Power of Attorney (filed with the initial filing of the Annual Report on Form 10-K for the year ended June 30, 2011).                                                                                                                                                          |
| 31.1  | Section 302 Certification of Chief Executive Officer.                                                                                                                                                                                                                          |
| 31.2  | Section 302 Certification of Chief Financial Officer.                                                                                                                                                                                                                          |
| 32.1  | Section 906 Certification of Chief Executive Officer and Chief Financial Officer.                                                                                                                                                                                                   |

| * | Confidential treatment has been granted as to certain portions of this agreement. |
|---|-----------------------------------------------------------------------------------|
| + | Indicates a management contract or compensatory plan or arrangement.              |

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