Exhibit
10.4


Confidential Materials omitted and filed separately
with the


Securities and Exchange
Commission.  Asterisks denote omissions.


THIRD
AMENDMENT TO THE OCTOBER 31, 2002 LICENSE


This Third Amendment,
effective as of the date set forth above the signatures of the parties below,
pertains to the Exclusive Patent License Agreement, effective on October 31,
2002, as subsequently amended by a First Amendment on November 15, 2002
and a Second Amendment on July 17, 2004, by and between the Massachusetts Institute of Technology (“M.I.T.”) and
Momenta Pharmaceuticals, Inc. (“COMPANY”).


WHEREAS, COMPANY possesses certain non-exclusive
rights and desires to obtain certain exclusive rights to M.I.T. Case No. 6582, “A
Method for the Mass Spectrometric Determination of the Molecular Weight of
Highly Acidic (and Basic) Organic and Biological Molecules,” by Klaus Biemann
and Peter Juhasz; and


WHEREAS. M.I.T. is willing to grant such rights to
COMPANY;


NOW, THEREFORE, M.I.T. and
COMPANY hereby agree to modify the Exclusive Patent License Agreement as
follows:


1.               The first paragraph of Section 2.2, as
amended, shall be modified to read as follows:


2.2   Exclusivity.
In order to establish an exclusive period for COMPANY and its AFFILIATES,
M.I.T. agrees that it shall not grant any other license for PATENTS RIGHTS
HEPARINASE, PATENT RIGHTS MASSPEC, PATENT RIGHTS SEQUENCING and PATENT RIGHTS
ENZYMES in FIELD SEQUENCING MACHINES to develop, make, have made, use, sell,
offer to sell, lease and import LICENSED PRODUCTS during the TERM.


2.               The last sentence of Section 2.2, as amended,
shall be amended to read as follows:


Upon COMPANY’s exercise of such right, the Appendix of this Agreement
that describes the PATENT RIGHTS that dominate the IMPROVEMENT shall be deemed
to have been amended to add the invention disclosure (and any related patent
applications) covering such IMPROVEMENT, and such IMPROVEMENT and any resulting
patent applications and patents shall thereafter be included in PATENT RIGHTS
for all purposes of this Agreement, without any additional fee, other than the
one Ten Thousand Dollar fee referred to in the previous sentence, and M.I.T.
shall provide COMPANY with an updated Appendix A, B, C or E for its
records.


3.               Section 7.2(a), as amended, shall be modified
to read as follows:


COMPANY Right to Prosecute PATENT RIGHTS in Exclusive Fields.  So
long as COMPANY remains the exclusive licensee of the PATENT RIGHTS SEQUENCING,
PATENT RIGHTS MASSPEC, PATENT RIGHTS HEPARINSE and PATENT RIGHTS ENZYMES in the
FIELD SEQUENCING MACHINES in the TERRITORY, COMPANY, to the extent permitted by
law, shall have the right, under its own control and at its own expense, to
prosecute any third party infringement of the PATENT RIGHTS SEQUENCING, PATENT
RIGHTS MASSPEC, PATENT RIGHTS HEPARINASE and









 



PATENT RIGHTS ENZYMES in the FIELD SEQUENCING MACHINES in the
TERRITORY, subject to Sections 7.4 and 7.5.  If required by law, M.I.T. shall permit any
action under this Section to be brought in its name, including being joined as
a party-plaintiff, provided that COMPANY shall hold M.I.T. harmless from, and
indemnify M.I.T. against, any costs, expenses, or liability that M.I.T. incurs
in connection with such action.  Prior to
commencing any such action, COMPANY shall consult with M.I.T. and shall consider
the views of M.I.T. regarding the advisability of the proposed action and its
effect on the public interest.  COMPANY
shall not enter into any settlement, consent judgment, or other voluntary final
disposition of any infringement action under this Section without the prior
written consent of M.I.T.


4.               Section 7.2(c) shall be deleted in its
entirety.


5.               Section 7.7, as amended, shall be modified to
read as follows:


Right to Sublicense.  So long as COMPANY remains the
exclusive licensee of the PATENT RIGHTS SEQUENCING, PATENT RIGHTS MASSPEC,
PATENT RIGHTS HEPARINASE and PATENT RIGHTS ENZYMES in the FIELD SEQUENCING
MACHINES in the TERRITORY, COMPANY shall have the sole right to sublicense any
alleged infringer in the FIELD SEQUENCING MACHINES in the TERRITORY for future
use of the PATENT RIGHTS SEQUENCING, PATENT RIGHTS MASSPEC, PATENT RIGHTS
HEPARINASE and PATENT RIGHTS ENZYMES in accordance with the terms and
conditions of this Agreement relating to sublicenses.  Any upfront fees as part of such sublicense
shall be shared equally between COMPANY and M.I.T.; other revenues to COMPANY
pursuant to such sublicense shall be treated as set forth in Article 4.


6.               In consideration of
the exclusive license granted for PATENT RIGHTS MASSPEC in the FIELD SEQUENCING
MACHINES hereunder, COMPANY shall pay M.I.T. a license expansion fee of [**]
Dollars ($[**]), which shall be due upon the Effective Date of this Third
Amendment.


All other terms and
conditions of the License Agreement shall remain unchanged.


The
EFFECTIVE DATE of this Amendment is August 5, 2006.


Agreed
to for:


	
  MASSACHUSETTS INSTITUTE OF

  	
   

  	
  MOMENTA PHARMACEUTICALS, INC

  
	
  TECHNOLOGY

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
  By

  	
    /s/Lita
  L. Nelsen

  	
   

  	
   

  	
  By

  	
    /s/Susan
  K. Whoriskey, Ph.D.

  	
   

  
	
  Name:

  	
  Lita L. Nelsen

  	
   

  	
   

  	
  Name:

  	
  Susan K. Whoriskey, Ph.D.

  	
   

  
	
  Title:

  	
  Director,
  Technology Licensing Office

  	
   

  	
   

  	
  Title:

  	
  Vice President, Licensing &

  	
   

  
	
  Date :

  	
  August 3, 2006

  	
   

  	
   

  	
  Business Development

  	
   

  
	
   

  	
   

  	
   

  	
   

  	
  Date:

  	
  August 3, 2006

  	
   

  
													



 



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