Document:

<Page>

                                                            Exhibit 10.16

          Confidential Materials omitted and filed separately with the
         Securities and Exchange Commission. Asterisks denote omissions.

February 1, 2005

Dennis P. Bauer, Ph.D.
Siegfried (USA), Inc.
33 Industrial Park Road
Pennsville, NJ 08070

Dear Dennis:

Reference is made to the Development and Production Agreement for Active
Pharmaceutical Ingredient between Siegfried (USA), Inc. and Siegfried Ltd.
("SIEGFRIED") and Momenta Pharmaceuticals, Inc. ("MOMENTA") dated October 10,
2003, as amended or supplemented by Letter Agreement dated February 14, 2004,
May 17, 2004, September 29, 2004 and January 26, 2005 (the "Agreement").
Capitalized terms used herein and not otherwise defined shall have the meanings
given such terms in the Agreement.

Pursuant to the Letter Agreement dated September 29, 2004, MOMENTA engaged
SIEGFRIED to undertake the CONTINUING DEVELOPMENT WORK on a time and materials
basis for work authorized by MOMENTA. MOMENTA and SIEGFRIED hereby agree that
for all CONTINUING DEVELOPMENT WORK performed on or after December 1, 2004,
SIEGFRIED shall invoice MOMENTA for the number of FTEs (full-time equivalent
person years) actually devoted to CONTINUING DEVELOPMENT WORK at an annual rate
equal to [**] Dollars ($[**]) per FTE. All other terms and conditions of the
Agreement shall remain in full force and effect, including, without limitation,
SIEGFRIED's obligation to invoice MOMENTA monthly for CONTINUING DEVELOPMENT
WORK and SIEGFRIED's obligation to provide MOMENTA with a detailed accounting
for the month of the CONTINUING DEVELOPMENT WORK.

<Page>

Dennis P. Bauer, Ph.D.
February 1, 2005
Page 2 of 2

If the foregoing is in conformity with your understanding, please execute both
copies of this Letter Agreement and return one fully-executed copy to me.

                                     Very truly yours,

                                     /s/ John E. Bishop
                                     John E. Bishop
                                     Vice President, Pharmaceutical Services &
                                     Manufacturing

Agreed and accepted:

SIEGFRIED (USA), INC.

By:  [illegible]
   -----------------------

SIEGFRIED LTD.

By:  /s/ Dennis P. Bauer
   -----------------------<Page>

                                                               Exhibit 10.17

          Confidential Materials omitted and filed separately with the
         Securities and Exchange Commission. Asterisks denote omissions.

February 11, 2005

Dr. John E. Bishop
Vice President, Pharmaceutical Sciences & Manufacturing
Momenta Pharmaceuticals, Inc.
675 West Kendall St.
Cambridge, MA 02142

Dear John:

Reference is made to the Development and Production Agreement for Active
Pharmaceutical Ingredient between Siegfried (USA), Inc. and Siegfried Ltd.
(collectively, "SIEGFRIED") and Momenta Pharmaceuticals, Inc. ("MOMENTA") dated
October 10, 2003, as amended or supplemented by letter agreements dated February
14, 2004, May 17, 2004, September 29, 2004, January 26, 2005 and February 1,
2005 (the "Agreement"). Capitalized terms used herein and not otherwise defined
shall have the meanings given such terms in the Agreement.

MOMENTA hereby authorizes SIEGFRIED's purchase and installation of the
manufacturing equipment identified below for the manufacture of the PRODUCT. The
purchase and installation of the manufacturing equipment shall be deemed to have
been conducted under the terms and conditions of the Agreement, with the
following modifications:

     1.   SIEGFRIED shall purchase [**] (quotation attached) previously agreed
          upon by MOMENTA and SIEGFRIED (the "[**]") and [**].

     2.   SIEGFRIED shall order the [**] upon receipt of the signed copy of this
          letter and will install the [**] within two days of equipment receipt.

     3.   SIEGFRIED estimates the cost for the [**] (including the [**]) at [**]
          U.S. Dollars ($[**]). The cost breakdown is summarized as below:

<Table>
<Caption>
                 ITEM                               COST
                 ----------------------------------------------
                 <S>                               <C>
                 [**]                              $ [**]
                 [**]                              $ [**]
                 [**]                              $ [**]
                 ----------------------------------------------
                 Total                             $ [**]
                 ----------------------------------------------
</Table>

<Page>

     4.   During the term of the Agreement, SIEGFRIED will use the [**] only for
          the manufacture of the PRODUCT. However, should MOMENTA (or a
          collaborator of MOMENTA) and SIEGFIRED enter into an additional
          agreement(s) pertaining to the further manufacture of the PRODUCT
          and/or the manufacture of any other product and should the [**] be
          reasonably useful or necessary for the further manufacture of the
          PRODUCT and/or for the manufacture of the other product, during the
          term of such additional agreement(s), SIEGFRIED will use the [**] only
          for the manufacture of the PRODUCT and/or the manufacture of the other
          product.

     5.   MOMENTA shall reimburse SIEGFRIED for the actual costs of the [**]
          (including the [**]). In addition, MOMENTA shall reimburse SIEGFRIED
          the actual costs of purchasing [**] used in the manufacture of the
          PRODUCT. Invoicing and payment shall be in accordance with Section
          10.1 of the Agreement. For purposes of Section 9.4 of the Agreement,
          the foregoing fees shall be attributed to the [**].

     6.   At the termination of the Agreement, or any additional agreement(s),
          SIEGFRIED shall retain all title and claim to the [**].

If the foregoing is acceptable to MOMENTA, please indicate your consent below.

Best regards,

/s/ Scott Powers

Scott Powers
Manager, Business Development

Momenta Pharmaceuticals, Inc.

By:    /s/ John E. Bishop
       --------------------------------------------------------
Name:  John E. Bishop
Title: Vice President, Pharmaceutical Services & Manufacturing
Date:  February 11, 2005<Page>

                                                                   EXHIBIT 10.37

                        FIRST LOAN MODIFICATION AGREEMENT

            This First Loan Modification Agreement (this "Loan Modification
Agreement') is entered into as of December 28, 2004, by and between SILICON
VALLEY BANK, a California-chartered bank, with its principal place of business
at 3003 Tasman Drive, Santa Clara, California 95054 and with a loan production
office located at One Newton Executive Park, Suite 200, 2221 Washington Street,
Newton, Massachusetts 02462, doing business under the name "Silicon Valley East"
("Bank") and MOMENTA PHARMACEUTICALS, INC., a Delaware corporation with its
chief executive office located at 675 West Kendall Street, Cambridge,
Massachusetts 02142 ("Borrower").

1.    DESCRIPTION OF EXISTING INDEBTEDNESS AND OBLIGATIONS. Among other
indebtedness and obligations which may be owing by Borrower to Bank, Borrower is
indebted to Bank pursuant to a loan arrangement dated as of December 27, 2002,
evidenced by, among other documents, a certain Loan and Security Agreement dated
as of December 27, 2002, between Borrower and Bank (as amended, the "Loan
Agreement"). Capitalized terms used but not otherwise defined herein shall have
the same meaning as in the Loan Agreement.

2.    DESCRIPTION  OF  COLLATERAL.  Repayment of the  Obligations  is secured by
the Collateral as described in the Loan Agreement (together with any other
collateral security granted to Bank, the "Security Documents").

      Hereinafter, the Security Documents, together with all other documents
evidencing or securing the Obligations shall be referred to as the "Existing
Loan Documents".

3.    DESCRIPTION OF CHANGE IN TERMS.

      A.    Modifications to Loan Agreement.

            1.    The Loan Agreement shall be amended by deleting Section 4.1
                  entitled "Grant of Security Interest" in its entirety, and
                  substituting therefor Section 4.1, as it appears in the 2004
                  Loan Arrangement.

            2.    The Loan Agreement shall be amended by deleting Article 5
                  entitled "Representations and Warranties" in its entirety, and
                  substituting therefor Article 5, as it appears in the 2004
                  Loan Arrangement. The "Perfection Certificate" as defined in
                  Section 5.1, shall mean the updated Perfection Certificate
                  delivered on or about the date hereof.

            3.    The Loan Agreement shall be amended by deleting Article 6
                  entitled "Affirmative Covenants" in its entirety, and
                  substituting therefor Article 6, as it appears in the 2004
                  Loan Arrangement.

            4.    The Loan Agreement shall be amended by deleting Article 7
                  entitled "Negative Covenants" in its entirety, and
                  substituting therefor Article 7, as it appears in the 2004
                  Loan Arrangement.

            5.    The Loan Agreement shall be amended by deleting Section 8.4
                  entitled "Attachments" in its entirety, and substituting
                  therefor Section 8.4, as it appears in the 2004 Loan
                  Arrangement.

            6.    The Loan Agreement shall be amended by deleting Section 8.5
                  entitled "Insolvency" in its entirety, and substituting
                  therefor Section 8.5, as it appears in the 2004 Loan
                  Arrangement.

<Page>

            7.    The Loan Agreement shall be amended by deleting Section 8.6
                  entitled "Other Agreements" in its entirety, and substituting
                  therefor Section 8.6, as it appears in the 2004 Loan
                  Agreement.

            8.    The Loan Agreement shall be amended by deleting Section 8.7
                  entitled "Judgments" in its entirety, and substituting
                  therefor Section 8.7, as it appears in the 2004 Loan
                  Agreement.

            9.    The Loan Agreement shall be amended by inserting the following
                  Section 8.9 thereof, entitled "2004 SVB Loan Arrangement":

                  "8.9 2004 SVB LOAN ARRANGEMENT. The occurrence of an Event of
                  Default under the 2004 SVB Loan Arrangement."

            10.   The Loan Agreement shall be amended by deleting subsections
                  (c), (f) and (h) from Section 9.1 entitled "Rights and
                  Remedies" in its entirety.

            11.   The Loan Agreement shall be amended by deleting Section 9.2
                  entitled "Power of Attorney" in its entirety, and substituting
                  therefor Section 9.2, as it appears in the 2004 Loan
                  Arrangement.

            12.   The Loan Agreement shall be amended by deleting Section 9.3
                  entitled "Accounts Notification/Collection" in its entirety.

            13.   The Loan Agreement shall be amended by deleting the following
                  information of the Borrower, appearing in Section 10 entitled
                  "Notices" thereof:

                  If to Borrower:   Momenta Pharmaceuticals, Inc.
                                    23 Moulton Street
                                    Cambridge, Massachusetts 02138
                                    Attn: Ms. Susan Whoriskey
                                    FAX: (617) 491-9701

                  and inserting in lieu thereof the following:

                  If to Borrower:   Momenta Pharmaceuticals, Inc.
                                    675 West Kendall Street
                                    Cambridge, Massachusetts  02142
                                    Attn: Mr. Richard Shea, Chief Financial
                                          Officer
                                    FAX: (617) 621-0431

            14.   The Loan Agreement shall be amended by deleting Section 12.1
                  entitled "Successors and Assigns" in its entirety, and
                  substituting therefor Section 12.1, as it appears in the 2004
                  Loan Arrangement.

            15.   The Loan Agreement shall be amended by deleting Section 12.2
                  entitled "Indemnification" in its entirety, and substituting
                  therefor Section 12.2, as it appears in the 2004 Loan
                  Arrangement.

            16.   The Loan Agreement shall be amended by deleting Section 12.3
                  entitled "Right of Set-Off" in its entirety, and substituting
                  therefor Section 12.3, as it appears in the 2004 Loan
                  Arrangement.

            17.   The Loan Agreement shall be amended by inserting the following
                  definition to appear alphabetically in Section 13.1 thereof:

<Page>

                  ""2004 SVB LOAN ARRANGEMENT" is that certain Loan and Security
                  Agreement dated as of December 28, 2004, by and between
                  Borrower and Bank."

            18.   The Loan Agreement shall be amended by deleting the following
                  definitions appearing in Section 13.1 thereof:

                  ""COLLATERAL" is any and all properties, rights and assets of
                  the Borrower granted by the Borrower to Bank, now, or in the
                  future, in which the Borrower obtains an interest, or the
                  power to transfer rights, including, without limitation, the
                  property described and subject to the exclusions described on
                  EXHIBIT A."

                  ""CREDIT EXTENSIONS" is each Equipment Advance or any other
                  extension of credit by Bank for Borrower's benefit."

                  ""MATERIAL ADVERSE CHANGE " is: (i) A material impairment in
                  the perfection or priority of Bank's security interest in the
                  Collateral or in the value of such Collateral; (ii) a material
                  adverse change in the business, operations, or condition
                  (financial or otherwise) of the Borrower; or (iii) a material
                  impairment of the prospect of repayment of any portion of the
                  Obligations. "

                  ""OBLIGATIONS" are debts, principal, interest, Bank Expenses
                  and other amounts Borrower owes Bank now or later, under the
                  Loan Documents, and including interest accruing after
                  Insolvency Proceedings begin."

                  "PERMITTED INDEBTEDNESS" is:

                  (a)    Borrower's indebtedness to Bank under this Agreement or
                         the Loan Documents;

                  (b)    Indebtedness existing on the Closing Date and shown on
                         the Disclosure Schedule attached hereto;

                  (c)    Subordinated Debt;

                  (d)    Indebtedness to trade creditors incurred in the
                         ordinary course of business; and

                  (e)    Indebtedness secured by Permitted Liens; and

                  (f)    Extensions, refinancings, modifications, amendments and
                         restatements of any items of Permitted Indebtedness (a)
                         through (e) above, provided that the principal amount
                         thereof is not increased and the terms thereof are not
                         modified to impose more burdensome terms upon Borrower
                         or its Subsidiary, as the case may be.

                  (g)    Capital leases in an amount not to exceed One Hundred
                         Thousand Dollars, in the aggregate, during any fiscal
                         year; and

                  (h)    Loans to employees in an amount not to exceed Two
                         Hundred Fifty Thousand Dollars ($250,000.00), in the
                         aggregate, at any time."

                  ""PERMITTED LIENS" are:

                  (a)    Liens existing on the Closing Date and shown on the
                         Perfection Certificate or arising under this Agreement
                         or other Loan Documents;

<Page>

                  (b)    Liens for taxes, fees, assessments or other government
                         charges or levies, either not delinquent or being
                         contested in good faith and for which Borrower
                         maintains adequate reserves on its Books, if they have
                         no priority over any of Bank's security interests;

                  (c)    Purchase money Liens in amount not to exceed One
                         Hundred Thousand Dollars ($100,000.00), in the
                         aggregate during any fiscal year: (i) on Equipment
                         acquired or held by Borrower incurred for financing the
                         acquisition of the Equipment, or (ii) existing on
                         equipment when acquired, if the Lien is confined to the
                         property and improvements and the proceeds of the
                         equipment.

                  (d)    Leases or subleases and licenses or sublicenses granted
                         in the ordinary course of Borrower's business or
                         granted in connection with the consummation of
                         collaborations, joint ventures, or financing
                         arrangements with the Borrower's business partners in
                         the ordinary course of business, if the leases,
                         subleases, licenses and sublicenses permit granting
                         Bank a security interest; and

                  (e)    Liens incurred in the extension, renewal or refinancing
                         of the indebtedness secured by Liens described in (a)
                         through (d), but any extension, renewal or replacement
                         Lien must be limited to the property encumbered by the
                         existing Lien and the principal amount of the
                         indebtedness may not increase unless such increase is
                         itself Permitted Indebtedness."

                  ""RESPONSIBLE OFFICER" is each of the Chief Executive Officer
                  and Vice President for Licensing and Business Development of
                  Borrower."

                  and inserting in lieu thereof the following:

                  ""COLLATERAL" is any and all properties, rights and assets of
                  the Borrower as described on EXHIBIT A."

                  ""CREDIT EXTENSIONS" is each Equipment Advance or any other
                  extension of credit by Bank for Borrower's benefit, pursuant
                  to this Agreement."

                  ""MATERIAL ADVERSE CHANGE " is: (i) A material impairment in
                  the perfection or priority of Bank's security interest in the
                  Collateral or in the value of such Collateral; or (ii) a
                  material adverse change in the business, operations, or
                  condition (financial or otherwise) of the Borrower."

                  ""OBLIGATIONS" are debts, principal, interest, Bank Expenses
                  and other amounts Borrower owes Bank now or later under this
                  Agreement, or the 2004 SVB Loan Arrangement, including letters
                  of credit, cash management services, and foreign exchange
                  contracts, if any, and including interest accruing after
                  Insolvency Proceedings begin and debts, liabilities, or
                  obligations of Borrower assigned to Bank."

                  ""PERMITTED INDEBTEDNESS" is:

                  (a)    Borrower's indebtedness to Bank under this Agreement,
                         the 2004 SVB Loan Arrangement, or the Loan Documents;

                  (b)    Indebtedness existing on the Closing Date and shown on
                         the Perfection Certificate;

                  (c)    Subordinated Debt;

<Page>

                  (d)    Indebtedness to trade creditors incurred in the
                         ordinary course of business;

                  (e)    Indebtedness secured by Permitted Liens;

                  (f)    Extensions, refinancings, modifications, amendments and
                         restatements of any items of Permitted Indebtedness (a)
                         through (e) above, provided that the principal amount
                         thereof is not increased or the terms thereof are not
                         modified to impose more burdensome terms upon Borrower
                         or its Subsidiary, as the case may be;

                  (g)    Other Indebtedness not otherwise permitted by Section
                         7.4 not exceeding One Million Dollars ($1,000,000.00),
                         in the aggregate, outstanding at any time; and

                  (h)    Capital leases.

                  ""PERMITTED LIENS" are:

                  (a)    Liens existing on the Closing Date and shown on the
                         Perfection Certificate or arising under this Agreement
                         or other Loan Documents;

                  (b)    Liens for taxes, fees, assessments or other government
                         charges or levies, either not delinquent or being
                         contested in good faith and for which Borrower
                         maintains adequate reserves on its Books;

                  (c)    Purchase money Liens (i) on Equipment acquired or held
                         by Borrower incurred for financing the acquisition of
                         the Equipment (now or in the future), or (ii) existing
                         on equipment when acquired, IF the Lien is confined to
                         the property and improvements and the proceeds of the
                         equipment;

                  (d)    Leases or subleases and licenses or sublicenses granted
                         in the ordinary course of Borrower's business or
                         granted in connection with the consummation of
                         collaborations, joint ventures, or financing
                         arrangements with the Borrower's business partners in
                         the ordinary course of business; and

                  (e)    Liens incurred in the extension, renewal or refinancing
                         of the indebtedness secured by Liens described in (a)
                         through (d), BUT any extension, renewal or replacement
                         Lien must be limited to the property encumbered by the
                         existing Lien and the principal amount of the
                         indebtedness may not increase."

                  ""RESPONSIBLE OFFICER" is each of the Chief Executive Officer
                  and Chief Financial Officer of Borrower."

            19.   The Loan Agreement shall be amended by deleting the
                  definitions of "Accounts", "Capitalization Event",
                  "Intellectual Property", "Inventory", and "Permitted
                  Investments" from Section 13.1.

            20.   The Collateral description appearing as EXHIBIT A to the Loan
                  Agreement is hereby replaced with the Collateral description
                  attached as EXHIBIT A hereto.

            21.   The Compliance Certificate appearing as EXHIBIT C to the Loan
                  Agreement is hereby deleted.

            22.   Terms that are capitalized in the Loan Agreement, but are not
                  otherwise defined, shall have the same meanings as set forth
                  in the 2004 SVB Loan Arrangement.

<Page>

      B.    Waivers.

            The financial reporting requirement set forth in former Section
            6.2(b) hereof for the months ended July 30, 2004, August 31, 2004,
            and October 31, 2004 are hereby waived, effective as of July 30,
            2004. Bank's waiver of Borrower's compliance of said financial
            reporting requirement shall apply only to the foregoing specific
            periods

4.    FEES. The Borrower shall reimburse Bank for all legal fees and expenses
incurred in connection with this amendment to the Existing Loan Documents.

5.    CONSISTENT CHANGES. The Existing Loan Documents are hereby amended
wherever necessary to reflect the changes described above.

6.    RATIFICATION OF LOAN DOCUMENTS. Borrower hereby ratifies, confirms, and
reaffirms all terms and conditions of all security or other collateral granted
to the Bank subject to amendment to the definition of Collateral, and confirms
that the indebtedness secured thereby includes, without limitation, the
Obligations.

7.    NO DEFENSES OF BORROWER. Borrower hereby acknowledges and agrees that
Borrower has no offsets, defenses, claims, or counterclaims against Bank with
respect to the Obligations, or otherwise, and that if Borrower now has, or ever
did have, any offsets, defenses, claims, or counterclaims against Bank, whether
known or unknown, at law or in equity, all of them are hereby expressly WAIVED
and Borrower hereby RELEASES Bank from any liability thereunder.

8.    CONTINUING VALIDITY. Borrower understands and agrees that in modifying the
existing Obligations, Bank is relying upon Borrower's representations,
warranties, and agreements, as set forth in the Existing Loan Documents. Except
as expressly modified pursuant to this Loan Modification Agreement, the terms of
the Existing Loan Documents remain unchanged and in full force and effect.
Bank's agreement to modifications to the existing Obligations pursuant to this
Loan Modification Agreement in no way shall obligate Bank to make any future
modifications to the Obligations. Nothing in this Loan Modification Agreement
shall constitute a satisfaction of the Obligations. It is the intention of Bank
and Borrower to retain as liable parties all makers of Existing Loan Documents,
unless the party is expressly released by Bank in writing. No maker will be
released by virtue of this Loan Modification Agreement.

9.    COUNTERSIGNATURE. This Loan Modification Agreement shall become effective
only when it shall have been executed by Borrower and Bank (provided, however,
in no event shall this Loan Modification Agreement become effective until signed
by an officer of Bank in California).

            [THE REMAINDER OF THIS PAGE IS INTENTIONALLY LEFT BLANK]

<Page>

            This Loan Modification Agreement is executed as a sealed instrument
under the laws of the Commonwealth of Massachusetts as of the date first written
above.

   BORROWER:                                          BANK:

   MOMENTA PHARMACEUTICALS, INC.                      SILICON VALLEY BANK, doing
                                                      business as
                                                      SILICON VALLEY EAST

   By:  /s/ Richard P. Shea                           By:  /s/ R. Bryan Jadot
        -------------------                                ------------------

   Name: Richard P. Shea                              Name: R. Bryan Jadot
         ---------------                                    --------------

   Title: Vice President and Chief Financial Officer  Title: Vice President
          ------------------------------------------         --------------

                                                      SILICON VALLEY BANK

                                                      By: [illegible]
                                                          -----------

                                                      Name: [illegible]
                                                            -----------

                                                      Title: Loan Ops Supervisor
                                                             -------------------
                                                          (signed in Santa Clara
                                                          County, California)

<Page>

                                    EXHIBIT A

     The Collateral consists of all of Borrower's right, title and interest in
and to the following:

     1.     Each item of equipment, or personal property financed with a
"Equipment Advance" pursuant to that certain Loan and Security Agreement, dated
as of December 27, 2002 (the "Loan Agreement"), by and between Borrower and
Bank, including, without limitation, the property described in ANNEX A hereto,
whether now owned or hereafter acquired, together with all substitutions,
renewals or replacements of and additions, improvements, and accessions to any
and all of the foregoing, and all proceeds from sales, renewals, releases or
other dispositions thereof.

     2.     All Borrower's books relating to the foregoing and any and all
claims, rights and interest in any of the above and all substitutions for,
additions, attachments, accessories, accessions and improvements to and
replacements, products, proceeds and insurance proceeds of any or all of the
foregoing.

<Page>

                              ANNEX A TO EXHIBIT A

     The Financed Equipment being financed with the Equipment Advance is listed
below. Upon the funding of such Equipment Advance, this schedule automatically
shall be deemed to be a part of the Collateral.

<Table>
<Caption>
      Description of Equipment            Make               Model                 Serial#        Invoice#
      ----------------------------------------------------------------------------------------------------
      <S>                                 <C>                <C>                   <C>            <C>

</Table>

Source: [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00082-of-00352.parquet"}, [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00082-of-00352.parquet"}], [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00082-of-00352.parquet"}]]