Exhibit 10.1

GILEAD SCIENCES, INC.

CODE SECTION 162(m) BONUS PLAN

As Amended and Restated Effective January 1, 2011

1. Purpose of the Plan. The purpose of the Plan is to provide a link between
compensation and performance, to motivate participants to achieve corporate
performance objectives and to enable the Company to attract and retain high
quality Eligible Employees.

2. Definitions. As used herein, the following definitions shall apply:

(a) “Board” means the Board of Directors of the Company.

(b) “Bonus” means a cash payment made pursuant to the Plan.

(c) “Code” means the Internal Revenue Code of 1986, as amended.

(d) “Committee” means the Compensation Committee of the Board.

(e) “Company” means Gilead Sciences, Inc., a Delaware corporation.

(f) “Corporate Bonus Plan” means the Gilead Sciences, Inc. Corporate Bonus Plan,
as amended from time to time.

(g) “Covered Employee” means an Employee who is a “covered employee” under
Section 162(m) of the Code.

(h) “Director” means a non-Employee member of the Board.

(i) “Eligible Employee” means an Employee who holds the title of Senior Vice
President or above and who would in the absence of such title and position be
eligible to participate in the Corporate Bonus Plan.

(j) “Employee” means any person who is in the employ of the Company, subject to
the control and direction of the Company as to both the work to be performed and
the manner and method of performance. Neither service as a Director nor fees
received from the Company for service as a Director shall be sufficient to
constitute Employee status.

(k) “Performance-Based Compensation” means compensation qualifying as
“performance-based compensation” under Section 162(m) of the Code.

(l) “Performance Goal” means any measurable criterion tied to the success of the
Company and based on one or more of the business criteria described in
Section 7.

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(m) ““Performance Period” means a period which may range in duration from a
minimum period of twelve (12) months to a maximum period of thirty-six
(36) months and over which the attainment of the applicable Performance Goals
set by the Committee is to be measured. The initial Performance Period under the
January 1, 2011 restatement of the Plan shall be the twelve (12)-month period
coincident with the Company’s 2011 fiscal year beginning January 1, 2011 and
ending December 31, 2011.

(n) “Plan” means the Gilead Sciences, Inc. Code Section 162(m) Bonus Plan, as
hereby amended and restated effective January 1, 2011.

3. Administration of the Plan.

(a) The Committee. The Plan shall be administered by the Committee (or a
subcommittee of the Committee) which shall be comprised solely of two or more
Directors eligible to serve on a committee awarding Bonus payments qualifying as
Performance-Based Compensation.

(b) Powers of the Committee. Subject the provisions of the Plan (including any
other powers given to the Committee hereunder), the Committee shall have the
authority, in its discretion, to:

(i) establish the duration of each Performance Period;

(ii) select the Eligible Employees who are to participate in the Plan for such
Performance Period;

(iii) determine the specific Performance Goal or Goals for each Performance
Period and the relative weighting of those goals, establish one or more
designated levels of attainment for those goals and set the Bonus potential for
each participant at each corresponding level of attainment;

(iv) certify the level at which the applicable Performance Goal or Goals are
attained for the Performance Period and determine, on the basis of that
certification, the actual Bonus for each participant in an amount not to exceed
his or her maximum Bonus potential for the certified level of attainment;

(v) exercise discretionary authority, when appropriate, to reduce the actual
Bonus payable to any participant below his or her Bonus potential for the
attained level of the Performance Goal(s) for the Performance Period;

(vi) construe and interpret the terms of the Plan and Bonuses awarded under the
Plan;

(vii) establish additional terms, conditions, rules or procedures for the
administration of the Plan; provided, however, that no Bonus shall be awarded
under any such additional terms, conditions, rules or procedures with terms or
conditions which are inconsistent with the provisions of the Plan; and

 

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(viii) take such other action, not inconsistent with the terms of the Plan, as
the Committee deems appropriate.

(c) Indemnification. In addition to such other rights of indemnification as they
may have as members of the Board, members of the Committee who administer the
Plan shall be defended and indemnified by the Company, to the extent permitted
by law, on an after-tax basis against (i) all reasonable expenses (including
attorneys’ fees) actually and necessarily incurred in connection with the
defense of any claim, investigation, action, suit or proceeding, or in
connection with any appeal therein, to which they or any of them may be a party
by reason of any action taken or failure to act under or in connection with the
Plan or any Bonus awarded hereunder and (ii) all amounts paid by them in
settlement thereof (provided such settlement is approved by the Company) or paid
by them in satisfaction of a judgment in any such claim, investigation, action,
suit or proceeding, except in relation to matters as to which it shall be
adjudged in such claim, investigation, action, suit or proceeding that such
person is liable for gross negligence, bad faith or intentional misconduct;
provided, however, that within 30 days after the institution of such claim,
investigation, action, suit or proceeding, such person shall offer to the
Company, in writing, the opportunity at the Company’s expense to handle and
defend the same.

4. Coverage. All Eligible Employees shall be covered by the Plan, except to the
extent the Committee may elect to exclude one or more Eligible Employees from
participation in a designated Performance Period.

5. Coordination with Corporate Bonus Plan; No Duplication of Benefits. While
this Plan is in effect, Eligible Employees participating in this Plan shall not
be eligible to participate in the Corporate Bonus Plan. Administration of the
Bonuses awarded under this Plan shall be governed by reference to the terms and
conditions of the Corporate Bonus Plan, but such reference is intended solely as
a means of administering this Plan and the Corporate Bonus Plan in a similar
manner, subject, however, to all of the limitations on and procedures applicable
to Bonuses set forth in this Plan document. To the extent the terms and
conditions set forth in this Plan document are in conflict with those of the
Corporate Bonus Plan or are required to apply in order for Bonuses to qualify as
Performance-Based Compensation, the terms and conditions set forth in this Plan
document shall control.

6. Terms and Conditions of Bonus Awards.

(a) Pre-Established Performance Goals. Payment of Bonuses shall be based solely
on account of the attainment of one or more pre-established, objective
Performance Goals over the designated Performance Period. The Committee shall
establish one or more objective Performance Goals with respect to each Eligible
Employee in writing not later than 90 days after the commencement of the
Performance Period to which the Performance Goals relate, provided that the
outcome of the Performance Goals is substantially uncertain at the time of their
establishment. Performance Goals shall be based solely on one or more of the
business criteria described in the Section 7 and shall be weighted, equally or
in such other proportion as the Committee shall determine at the time such
Performance Goals are established, for purposes of determining the actual Bonus
amounts that may become payable upon the attainment of those goals.

 

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(b) For each Performance Goal, the Committee may establish one or more
designated levels of attainment and set the Bonus potential for each Eligible
Employee at each designated performance level. Alternatively, the Committee may
establish a linear formula for determining the Bonus potential at various points
of Performance Goal attainment. Under no circumstance, however, shall the
aggregate Bonus potential for any participant for any Performance Period exceed
the applicable maximum dollar amount set forth in Section 6(e).

(c) Committee Certification. As soon as administratively practicable following
the completion of the Performance Period, the Committee shall certify the actual
levels at which the Performance Goal or Goals for that period have been attained
and determine, on the basis of such certified levels, the actual Bonus amount to
be paid to each Eligible Employee for that Performance Period. Payment of such
Bonus amounts shall be made as soon as administratively thereafter, but in no
event earlier than the first day of the first fiscal year of the Company (the
“Post-Performance Fiscal Year”) following the fiscal year in which the
Performance Period is completed and no later than the last day of that
Post-Performance Fiscal Year, unless an earlier payment date for those Bonuses
would not result in the contravention of any applicable requirements under
Section 409A of the Code.

(d) Committee Discretion. The Committee, in determining the amount of the Bonus
actually to be paid to an Eligible Employee, shall in no event award a Bonus in
excess of the dollar amount determined on the basis of the Bonus potential
established for the particular level at which each of the applicable Performance
Goals for the Performance Period is attained. If the actual level of attainment
is between two of the designated performance levels, the Bonus amounts will be
interpolated on a straight-line basis. In addition, the Committee shall have the
discretion to reduce or eliminate the Bonus that would otherwise be payable with
respect to one or more Performance Goals on the basis of the certified level of
attained performance of those goals. The exercise of such discretion to decrease
the amount of a Bonus may be based on such performance criteria as may have been
established under the Corporate Bonus Plan or on such other criteria as the
Committee may choose to apply, including (without limitation) individual
performance. The Committee shall not waive any Performance Goal applicable to a
participant’s Bonus potential for a particular Performance Period, except under
such circumstances as the Committee deems appropriate in the event a Change in
Control should occur prior to the completion of that Performance Period. For
purposes of the Plan, a Change in Control shall have the same definition as set
forth in the Company’s 2004 Equity Incentive Plan (or any successor to that
plan).

(e) Individual Limitations on Awards. Notwithstanding any other provision of the
Plan, the maximum amount of any Bonus paid to a Covered Employee under the Plan
shall be limited to Seven Million Dollars ($7,000,000) per each twelve
(12)-month period (or portion thereof) included within the applicable
Performance Period.

(f) Payment Date. No participant shall accrue any right to receive a Bonus award
under the Plan unless that participant remains in Employee status until the
payment date for that Bonus following the completion of the Performance Period.
Accordingly, no Bonus payment shall be made to any participant who ceases
Employee status prior to the payment date for that Bonus; provided, however,
that the Committee shall have complete discretion to award a full or pro-rated
Bonus, based on the level at which the applicable Performance Goals are

 

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attained for the Performance Period, to a participant who ceases Employee status
prior to such payment date by reason of death or disability. A participant may
also defer the payment of the Bonus pursuant to the terms and conditions of the
Company’s Deferred Compensation Plan (or any successor plan) and in compliance
with Section 409A of the Code

7. Business Criteria.

(a) Permitted Criteria. Performance Goals established by the Committee may be
based on any one of, or combination of, the following: (i) revenue,
(ii) achievement of specified milestones in the discovery and development of one
or more of the Company’s products, (iii) achievement of specified milestones in
the commercialization of one or more of the Company’s products, (iv) achievement
of specified milestones in the manufacturing of one or more of the Company’s
products, (v) expense targets, (vi) share price (including, but not limited to,
growth measures and total shareholder return), (vii) earnings per share,
(viii) operating margin, (ix) gross margin, (x) return measures (including, but
not limited to, return on assets, capital, equity, or sales), (xi) net sales
growth, (xii) productivity ratios, (xiii) operating income, (xiv) net operating
profit, (xv) net earnings or net income (before or after taxes), (xvi) cash flow
(including, but not limited to, operating cash flow, free cash flow, and cash
flow return on capital), (xvii) earnings before or after interest, taxes,
depreciation, amortization and/or stock-based compensation expense,
(xviii) economic value added, (xix) market share, and (xx) working capital
targets. Such Performance Goals may measured not only in terms of the Company’s
performance but also in terms of its performance relative to the performance of
other entities or may be measured on the basis of the performance of any of the
Company’s business units or divisions or any parent or subsidiary entity.

(b) Authorized Adjustments. The Committee is authorized to make adjustments in
calculating the attained level of the applicable Performance Goals for a
Performance Period as follows: (i) exclude restructuring and/or other
non-recurring charges; (ii) exclude exchange rate effects, as applicable, for
non-U.S. dollar denominated net sales and operating earnings; (iii) exclude the
effects of changes to generally accepted accounting principles required by the
Financial Accounting Standards Board; (iv) exclude the effects of statutory
adjustments to corporate tax rates; (v) exclude the effects of “extraordinary
items” as determined under generally accepted accounting principles;
(vi) exclude any other unusual, non-recurring gain or loss or other
extraordinary item; (vii) adjust for the effects of any unusual or extraordinary
corporate item, transaction, event or development; (viii) adjust for the effects
of any changes in applicable laws, regulations, accounting principles or
business conditions; (ix) exclude the dilutive effects of acquisitions or joint
ventures; (x) assume that any business divested by the Company achieved
Performance Goals at targeted levels during the balance of a Performance Period
following such divestiture; (xi) exclude the effect of any change in the
outstanding shares of common stock of the Company by reason of any stock
dividend or split, stock repurchase, reorganization, recapitalization, merger,
consolidation, spin-off, combination or exchange of shares or other similar
corporate change, or any distribution to common stockholders other than regular
cash dividends; (xii) adjust for the effects of any corporate transaction, such
as a merger, consolidation, separation (including spin-off or other distribution
of stock or property by a corporation), or reorganization (whether or not such
reorganization comes within the definition of such term in Section 368 of the
Code); and (xiii) adjust for the effects of any partial or complete corporate
liquidation.

 

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8. Effective Date and Term of Plan. The Plan initially became effective on
January 1, 2006, and this restatement of the Plan is effective as of January 1,
2011, but no Bonus shall be paid under this restated Plan to a Covered Employee
unless the restated Plan is approved by the Company stockholders at the 2011
annual meeting. Assuming that such stockholder approval is obtained, the
restated Plan shall continue in effect until the Board terminates it or until
stockholder approval again is required for the restated Plan to meet the
requirements of Code Section 162(m) but is not obtained.

9. Amendment, Suspension or Termination of the Plan. The Board may at any time
amend, suspend or terminate the Plan. However, any amendment or modification of
the Plan shall be subject to stockholder approval to the extent required under
Code Section 162(m) or other applicable law or regulation.

10. General Provisions.

(a) Neither the action of the Company in establishing or maintaining the Plan,
nor any action taken under the Plan by the Committee, nor any provision of the
Plan itself shall be construed so as to grant any person the right to remain in
Employee status for any period of specific duration, and each participant shall
at all times remain an Employee at-will and may accordingly be discharged at any
time, with or without cause and with or without advance notice of such
discharge.

(b) No participant in the Plan shall have the right to transfer, alienate,
pledge or encumber his or her interest in the Plan, and such interest shall not
(to the maximum permitted by law) be subject to the claims of the participant’s
creditors or to attachment, execution or other process of law. However, should a
participant die before payment is made of the actual Bonus to which he or she
has become entitled under the Plan, then that Bonus shall be paid to the
executor or other legal representative of his or her estate.

(c) The terms and conditions of the Plan, together with the obligations and
liabilities of the Company that accrue hereunder, shall be binding upon any
successor to the Company, whether by way of merger, consolidation,
reorganization or other change in ownership or control of the Company

11. Unfunded Obligation. Eligible Employees eligible to participate in the Plan
shall have the status of general unsecured creditors of the Company. Any amounts
payable to such Employees pursuant to the Plan shall be unfunded and unsecured
obligations for all purposes, including (without limitation) Title I of the
Employee Retirement Income Security Act of 1974, as amended. The Company shall
not be required to segregate any monies from its general funds, or to create any
trusts, or establish any special accounts with respect to such obligations.
Employees shall have no claim against the Company for any changes in the value
of any assets that may be invested or reinvested by the Company with respect to
the Plan.

 

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