Document:

exv10w9

Exhibit 10.9

ALNYLAM PHARMACEUTICALS, INC.

Incentive Stock Option Agreement

Granted Under 2009 Stock Incentive Plan

1. Grant of Option.

     This agreement evidences the grant by Alnylam Pharmaceuticals, Inc,, a Delaware corporation
(the “Company”), on                      , 20[  ] (the “Grant Date”) to [                    ], an employee of the Company (the “Participant”), of an option to purchase, in whole or in
part, on the terms provided herein and in the Company’s 2009 Stock Incentive Plan (the “Plan”), a
total of [                    ] shares (the “Shares”) of common stock, $.0001 par value per
share, of the Company (“Common Stock”) at $[                    ] per Share. Unless earlier
terminated, this option shall expire at 5:00 p.m., Eastern time, on [                    ] (the “Final Exercise
Date”).

     It is intended that the option evidenced by this agreement shall be an incentive stock option
as defined in Section 422 of the Internal Revenue Code of 1986, as amended, and any regulations
promulgated thereunder (the “Code”). Except as otherwise indicated by the context, the term
“Participant”, as used in this option, shall be deemed to include any person who acquires the right
to exercise this option validly under its terms.

2. Vesting Schedule.

     This option will become exercisable (“vest”) as to 25% of the original number of Shares on the
first anniversary of the Grant Date and as to an additional 6.25% of the original number of Shares
at the end of each successive three-month period following the first anniversary of the Grant Date
until the fourth anniversary of the Grant Date.

     The right of exercise shall be cumulative so that to the extent the option is not exercised in
any period to the maximum extent permissible it shall continue to be exercisable, in whole or in
part, with respect to all Shares for which it is vested until the earlier of the Final Exercise
Date or the termination of this option under Section 3 hereof or the Plan.

3. Exercise of Option.

     (a) Form of Exercise. Each election to exercise this option shall be in writing,
signed by the Participant, and received by the Company at its principal office, accompanied by this
agreement, and payment in full in the manner provided in the Plan. The Participant may purchase
less than the number of shares covered hereby, provided that no partial exercise of this option may
be for any fractional share or for fewer than ten whole shares.

     (b) Continuous Relationship with the Company Required. Except as otherwise provided
in this Section 3, this option may not be exercised unless the Participant, at the time he or she
exercises this option, is, and has been at all times since the Grant Date, an employee or

 

 

officer of, or consultant or advisor to, the Company or any parent or subsidiary of the
Company as defined in Section 424(e) or (f) of the Code (an “Eligible Participant”).

     (c) Termination of Relationship with the Company. If the Participant ceases to be an
Eligible Participant for any reason, then, except as provided in paragraphs (d) and (e) below, the
right to exercise this option shall terminate three months after such cessation (but in no event
after the Final Exercise Date), provided that this option shall be exercisable only
to the extent that the Participant was entitled to exercise this option on the date of such
cessation. Notwithstanding the foregoing, if the Participant, prior to the Final Exercise Date,
violates the non-competition or confidentiality provisions of any employment contract,
confidentiality and nondisclosure agreement or other agreement between the Participant and the
Company, the right to exercise this option shall terminate immediately upon such violation.

     (d) Exercise Period Upon Death or Disability. If the Participant dies or becomes
disabled (within the meaning of Section 22(e)(3) of the Code) prior to the Final Exercise Date
while he or she is an Eligible Participant and the Company has not terminated such relationship for
“cause” as specified in paragraph (e) below, this option shall be exercisable, within the period of
one year following the date of death or disability of the Participant, by the Participant (or in
the case of death by an authorized transferee), provided that this option shall be
exercisable only to the extent that this option was exercisable by the Participant on the date of
his or her death or disability, and further provided that this option shall not be exercisable
after the Final Exercise Date.

     (e) Termination for Cause. If, prior to the Final Exercise Date, the Participant’s
employment is terminated by the Company for Cause (as defined below), the right to exercise this
option shall terminate immediately upon the effective date of such termination of employment.
“Cause” shall mean willful misconduct by the Participant or willful failure by the Participant to
perform his or her responsibilities to the Company (including, without limitation, breach by the
Participant of any provision of any employment, consulting, advisory, nondisclosure,
non-competition or other similar agreement between the Participant and the Company), as determined
by the Company, which determination shall be conclusive. The Participant’s employment shall be
considered to have been terminated for Cause if the Company determines, within 30 days after the
Participant’s resignation, that termination for Cause was warranted.

4. Tax Matters.

     (a) Withholding. No Shares will be issued pursuant to the exercise of this option
unless and until the Participant pays to the Company, or makes provision satisfactory to the
Company for payment of, any federal, state or local withholding taxes required by law to be
withheld in respect of this option.

     (b) Disqualifying Disposition. If the Participant disposes of Shares acquired upon
exercise of this option within two years from the Grant Date or one year after such Shares were
acquired pursuant to exercise of this option, the Participant shall notify the Company in writing
of such disposition.

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5. Transfer Restrictions. This option may not be sold, assigned, transferred, pledged or
otherwise encumbered by the Participant, either voluntarily or by operation of law, except by will
or the laws of descent and distribution, and, during the lifetime of the Participant, this option
shall be exercisable only by the Participant.

6. Provisions of the Plan.

     This option is subject to the provisions of the Plan (including the provisions relating to
amendments to the Plan), a copy of which is furnished to the Participant with this option.

     IN WITNESS WHEREOF, the Company has caused this option to be executed under its corporate seal
by its duly authorized officer. This option shall take effect as a sealed instrument.

	 	 	 	 	 
	 	ALNYLAM PHARMACEUTICALS, INC.

 	 
	 	By:  	 	 
	 	 	Name:  	 	 
	 	 	Title:  	 	 

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PARTICIPANT’S ACCEPTANCE

     The undersigned hereby accepts the foregoing option and agrees to the terms and conditions
thereof. The undersigned hereby acknowledges receipt of a copy of the Company’s 2009 Stock
Incentive Plan.

	 	 	 	 	 
	 	PARTICIPANT:

 	 
	 	 	 
	 	Address:  	 	 
	 	 	 	 

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ALNYLAM PHARMACEUTICALS, INC.

Nonstatutory Stock Option Agreement

Granted Under 2009 Stock Incentive Plan

1. Grant of Option.

     This agreement evidences the grant by Alnylam Pharmaceuticals, Inc., a Delaware corporation
(the “Company”), on                     , 20[  ] (the “Grant Date”) to [                    ], an [employee], [consultant], [director] of the Company (the “Participant”), of an option to
purchase, in whole or in part, on the terms provided herein and in the Company’s 2009 Stock
Incentive Plan (the “Plan”), a total of [                    ] shares (the “Shares”) of
common stock, $0001 par value per share, of the Company (“Common Stock”) at $[                    ]
per Share. Unless earlier terminated, this option shall expire at 5:00 p.m., Eastern time, on
[                    ] (the “Final Exercise Date”).

     It is intended that the option evidenced by this agreement shall not be an incentive stock
option as defined in Section 422 of the Internal Revenue Code of 1986, as amended, and any
regulations promulgated thereunder (the “Code”). Except as otherwise indicated by the context, the
term “Participant”, as used in this option, shall be deemed to include any person who acquires the
right to exercise this option validly under its terms.

2. Vesting Schedule.

     This option will become exercisable (“vest”) as to 25% of the original number of Shares on the
first anniversary of the Grant Date and as to an additional 6.25% of the original number of Shares
at the end of each successive three-month period following the first anniversary of the Grant Date
until the fourth anniversary of the Grant Date.

     The right of exercise shall be cumulative so that to the extent the option is not exercised in
any period to the maximum extent permissible it shall continue to be exercisable, in whole or in
part, with respect to all Shares for which it is vested until the earlier of the Final Exercise
Date or the termination of this option under Section 3 hereof or the Plan.

3. Exercise of Option.

     (a) Form of Exercise. Each election to exercise this option shall be in writing,
signed by the Participant, and received by the Company at its principal office, accompanied by this
agreement, and payment in full in the manner provided in the Plan. The Participant may purchase
less than the number of shares covered hereby, provided that no partial exercise of this option may
be for any fractional share or for fewer than ten whole shares.

     (b) Continuous Relationship with the Company Required. Except as otherwise provided
in this Section 3, this option may not be exercised unless the Participant, at the time he or she
exercises this option, is, and has been at all times since the Grant Date, an [employee, officer or
director of], or consultant or advisor to, the Company or any other entity the

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employees, officers, directors, consultants, or advisors of which are eligible to receive
option grants under the Plan (an “Eligible Participant”).

     (c) Termination of Relationship with the Company. If the Participant ceases to be an
Eligible Participant for any reason, then, except as provided in paragraphs (d) and (e) below, the
right to exercise this option shall terminate three months after such cessation (but in no event
after the Final Exercise Date), provided that this option shall be exercisable only
to the extent that the Participant was entitled to exercise this option on the date of such
cessation. Notwithstanding the foregoing, if the Participant, prior to the Final Exercise Date,
violates the non-competition or confidentiality provisions of any employment contract,
confidentiality and nondisclosure agreement or other agreement between the Participant and the
Company, the right to exercise this option shall terminate immediately upon such violation.

     (d) Exercise Period Upon Death or Disability. If the Participant dies or becomes
disabled (within the meaning of Section 22(e)(3) of the Code) prior to the Final Exercise Date
while he or she is an Eligible Participant and the Company has not terminated such relationship for
“cause” as specified in paragraph (e) below, this option shall be exercisable, within the period of
one year following the date of death or disability of the Participant, by the Participant (or in
the case of death by an authorized transferee), provided that this option shall be
exercisable only to the extent that this option was exercisable by the Participant on the date of
his or her death or disability, and further provided that this option shall not be exercisable
after the Final Exercise Date.

     (e) Termination for Cause. If, prior to the Final Exercise Date, the Participant’s
employment or other relationship with the Company is terminated by the Company for Cause (as
defined below), the right to exercise this option shall terminate immediately upon the effective
date of such termination of employment or other relationship. “Cause” shall mean willful
misconduct by the Participant or willful failure by the Participant to perform his or her
responsibilities to the Company (including, without limitation, breach by the Participant of any
provision of any employment, consulting, advisory, nondisclosure, non-competition or other similar
agreement between the Participant and the Company), as determined by the Company, which
determination shall be conclusive. The Participant’s employment or other relationship shall be
considered to have been terminated for “Cause” if the Company determines, within 30 days after the
Participant’s resignation, that termination for Cause was warranted.

4. Withholding.

     No Shares will be issued pursuant to the exercise of this option unless and until the
Participant pays to the Company, or makes provision satisfactory to the Company for payment of, any
federal, state or local withholding taxes required by law to be withheld in respect of this option.

5. Transfer Restrictions. This option may not be sold, assigned, transferred, pledged or
otherwise encumbered by the Participant, either voluntarily or by operation of law, except by will
or the laws of descent and distribution, and, during the lifetime of the Participant, this option
shall be exercisable only by the Participant.

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6. Provisions of the Plan.

     This option is subject to the provisions of the Plan (including the provisions relating to
amendments to the Plan), a copy of which is furnished to the Participant with this option.

     IN WITNESS WHEREOF, the Company has caused this option to be executed under its corporate seal
by its duly authorized officer. This option shall take effect as a sealed instrument.

	 	 	 	 	 
	 	ALNYLAM PHARMACEUTICALS, INC.

 	 
	 	By:  	 	 
	 	 	Name:  	 	 
	 	 	Title:  	 	 

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PARTICIPANT’S ACCEPTANCE

     The undersigned hereby accepts the foregoing option and agrees to the terms and conditions
thereof. The undersigned hereby acknowledges receipt of a copy of the Company’s 2009 Stock
Incentive Plan.

	 	 	 	 	 
	 	PARTICIPANT:

 	 
	 	 	 
	 	 	Address:  	 	 
	 	 	  	 	 

 - 8 -exv10w16

	 	 	 	 	 

Exhibit 10.16

Alnylam Pharmaceuticals, Inc.

2010 Annual Incentive Program

Summary Description

In February 2010, the Compensation Committee of the Board of Directors (the “Board”) of Alnylam
Pharmaceuticals, Inc. (“Alnylam” or the “Company”) established the 2010 Annual Incentive Program
(the “Bonus Plan”) to incent and reward eligible leadership employees based upon their performance
relative to pre-established 2010 corporate and individual goals and objectives, and retain company
leadership by establishing an important element of Alnylam’s total rewards package consistent with
Alnylam’s compensation philosophy and operating strategy.

Eligibility

Members of Alnylam’s Leadership Team, as defined by Alnylam’s Chief Executive Officer, including
the Chief Executive Officer, President and Chief Operating Officer, Vice Presidents, and Directors
and equivalent level leadership team members, that are employed by the Company before July 1, 2010
and on the day awards are granted under the Bonus Plan, are eligible to receive an annual cash
bonus based upon the achievement of individual and corporate goals and objectives for 2010
(collectively, “Plan Participants”).

Goals

The corporate goals for 2010 were proposed by the Company’s Executive Officers and approved by the
Board. Individual objectives focus on contributions that facilitate the achievement of the
Company’s corporate goals. The Compensation Committee approved the individual objectives for the
Company’s Executive Officers and Vice Presidents. The individual objectives for the other Plan
Participants have been approved by the Company’s Chief Executive Officer.

Awards

Awards under the Bonus Plan, if any, will be determined by first establishing a Plan Participant’s
individual award, which will be based upon performance against individual objectives for 2010.
Each Plan Participant has an established target opportunity under the Bonus Plan, as set forth in
the table below, representing a percentage of the Plan Participant’s base salary for 2010. The
individual award will range from 0% to 100% of the Plan Participant’s target opportunity (capped at
100% of the target opportunity) based upon the Plan Participant’s individual performance against
his or her 2010 objectives.

	 	 	 	 	 
	2010 Annual Incentive Program Target Opportunities	 
	Band - Title	 	Target Opportunity	 
	Chief Executive Officer
	 	 	50	%
	President and Chief Operating Officer
	 	 	30	%
	Senior Vice President/Vice President
	 	 	20	%
	Senior Director/Director
	 	 	12	%
	Associate Director
	 	 	7	%

 

 

     A corporate performance modifier will then be applied to the individual award. The
corporate performance modifier will range from 0% to 100% and will be based upon the Company’s
performance against the 2010 corporate goals; provided, however, that if corporate performance for
2010 falls below a threshold of 50%, the corporate performance modifier will be 0%. The
Compensation Committee retains the ability under the Bonus Plan to exercise its discretion in
adjusting an award higher or lower as it deems appropriate under the specific circumstances. At
the end of 2010, the Compensation Committee will evaluate individual and corporate performance
against the established goals and objectives and determine the amount of the awards, if any, to be
granted under the Bonus Plan. All awards under the Bonus Plan will be made in cash and paid in
January 2011.

Administration; Amendment

The Bonus Plan will be administered by the Compensation Committee of the Board. The Compensation
Committee shall have full power and authority to interpret and make all decisions regarding the
Bonus Plan, which decisions and interpretations shall be final and binding on all Plan
Participants. The Compensation Committee or the full Board may amend the Bonus Plan in any manner
at any time without the consent of any Plan Participant.

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