EX-10.4



 Exhibit 10.4 

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, $.01 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. Notwithstanding the foregoing, this
option will become fully exercisable in the event the Participant dies 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
Section 3(e) below. 
 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, $.01 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. Notwithstanding the foregoing,
this option will become fully exercisable in the event the Participant dies 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
Section 3(e) below. 
 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 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:	 	  

		 	  




  
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