<PAGE>

                                                                    EXHIBIT 10.7


                                AMENDMENT NO. 2

                                      TO

                               SUBORDINATED NOTE

                                      AND

                        COMMON STOCK PURCHASE AGREEMENT

                                 by and among

                              NMT MEDICAL, INC.,

                     WHITNEY SUBORDINATED DEBT FUND, L.P.

                           and, for certain purposes

                              J. H. WHITNEY & CO.

                         ____________________________


                              September 13, 1999


                         _____________________________
<PAGE>

                               AMENDMENT NO. 2 TO

                       SUBORDINATED NOTE AND COMMON STOCK
                               PURCHASE AGREEMENT


     This Amendment No. 2 to Subordinated Note and Common Stock Purchase
Agreement (this "Amendment"), dated as of September 13, 1999, by and among NMT
Medical, Inc. (f/k/a Nitinol Medical Technologies, Inc., ) ("Company"), a
Delaware corporation, Whitney Subordinated Debt Fund, L.P., ("Purchaser") and,
solely for the purposes of Sections 2.1 and 4(c) hereof, J.H. Whitney & Co.
("Whitney").

     WHEREAS, on July 8, 1998, the parties hereto entered into the Subordinated
Note and Common Stock Purchase Agreement (the "July 8, 1998 Agreement") and on
April 14, 1999 the Company and the Purchaser entered into Amendment No. 1 (the
"First Amendment") to the July 8, 1998 Agreement (the July 8, 1998 Agreement, as
amended by the First Amendment, the "Original Agreement");

     WHEREAS, contemporaneously with the execution of this Amendment, (a) the
Company, the other borrowers thereunder and Brown Brothers Harriman & Co. are
entering into a Credit Agreement (the "U.S. Credit Agreement"), and (b) NMT
NeuroSciences Implants (France) SA, the other borrower thereunder and Brown
Brothers Harriman & Co. are entering into a Credit Agreement (the "French Credit
Agreement" and together with the U.S. Credit Agreement, collectively, the
"Credit Agreement"), each dated September 13, 1999;

     WHEREAS, contemporaneously with the execution of this Amendment, the
Company and the other guarantors thereunder are entering into a Guarantee in
favor of Brown Brothers Harriman & Co. (the "Guarantee"), dated September 13,
1999;

     WHEREAS, a portion of the loan proceeds under the Credit Agreement together
with additional funds of the Company, shall be paid by the Company to Purchaser
upon the closing hereof, to be applied in payment of $14,000,000 of principal of
the WSDF Note and all unpaid accrued interest on the WSDF Note; and

     WHEREAS, the Company has requested and the Purchaser and Whitney have
agreed to amend the Original Agreement in order to, among other things, (i)
terminate all of the security interests granted by the Company to Purchaser
under the Original Agreement except as otherwise set forth herein, (ii) amend,
among other things, the principal amount of and the subordination provisions of
the WSDF Note, and (iii) amend various covenants contained in the Original
Agreement, all as hereinafter set forth.
<PAGE>

     NOW THEREFORE, in consideration of the premises set forth herein and for
other good and valuable consideration, the sufficiency and receipt of which is
hereby acknowledged, the parties hereto agree as follows:

                                   ARTICLE 1
                                  DEFINITIONS
                                  -----------

     1.1  Original Agreement Definitions.
          ------------------------------

          (a) All capitalized terms used in this Amendment but not defined shall
have the meanings given to them in the Original Agreement. In the event of a
conflict between the definitions contained in this Amendment and those contained
in the Original Agreement, the definitions contained herein shall prevail.

          (b) All references to the Note in the Original Agreement shall be
deemed to refer to the New Note (as defined below) from and after the date
hereof.

          (c) "Domestic Subsidiary" shall mean, each Subsidiary that is
incorporated or organized in the United States or any state or territory
thereof.

          (d) "Barclays Debt" shall mean, the outstanding Indebtedness of
Spembly Medical Ltd. to Barclays Bank plc in the principal amount as of the date
hereof of approximately (Pounds)180,000 pursuant to that certain Barclays
Treasury Loan Facility, dated as of April 15, 1996, by and between Spembly
Medical Ltd. and Barclays Bank plc.

          (e) "Senior Indebtedness" shall mean the principal of, premium, if
any, and interest (including any interest accruing subsequent to the filing of a
petition of bankruptcy at the rate provided for in the documentation with
respect hereto, whether or not such interest is an allowed claim under
applicable law) on, and all reasonable fees, reimbursement and indemnity
obligations, and all other obligations (collectively hereinafter referred to as
the "Obligations") arising under or in connection with the Credit Agreement, the
Guarantee or any instruments, agreements or documents issued or executed in
connection therewith, as the same may be amended from time to time thereafter,
together with any Obligations created or incurred in connection with one or more
restatements, renewals, extensions, restructurings, refundings, replacements or
refinancings of the Credit Agreement or the Guarantee; provided, however, that
                                                       --------  -------
the aggregate principal amount of Senior Indebtedness shall not exceed
$13,000,000.

                                       2
<PAGE>

                                   ARTICLE 2
                        AMENDMENTS TO ORIGINAL AGREEMENT
                        --------------------------------

     2.1  Termination of Security Interests and Amendments to Guarantee and
          -----------------------------------------------------------------
Collateral Agreement.
--------------------

          (a) Purchaser and Whitney hereby terminate and release all security
interests and interests in collateral granted to Purchaser and/or Whitney, in
any capacity, pursuant to the Pledge Agreements, which are hereby terminated,
and pursuant to or contemplated by the Guarantee and Collateral Agreement;

provided that, all other obligations of the Guarantors pursuant to the Guarantee
-------- ----
and Collateral Agreement shall continue in full force and effect, except as set
forth herein below to the contrary, and except that at any time during which
payment under the New Note may not be made pursuant to paragraph 7(a)(D)
thereof, such payment shall not be made by any Guarantor, and at any time during
which the exercise of remedies specified in paragraph 7(a)(E) of the New Note is
prohibited pursuant to said paragraph 7(a)(E), such remedies shall not be
exercised against any Guarantor, provided further that all such security
                                 -------- -------
interests and interests in collateral which are non-U.S. patents shall continue
in full force and effect and, subject to Brown Brothers Harriman & Co. and
Purchaser and/or Whitney entering into an agreement satisfactory to them (which
shall be without representation or warranty of any kind by Purchaser and/or
Whitney) shall be held by Purchaser and/or Whitney, as applicable, for the
benefit of Brown Brothers Harriman & Co..  Accordingly, any reference in the
Original Agreement or in the Guarantee and Collateral Agreement or in any other
document related thereto to the terms "collateral," "security," "security
interests," or any similar such term, for the benefit of Purchaser and/or
Whitney, shall be deemed of no further force or effect, except with respect to
the non-U.S. patents.  In furtherance of the foregoing, Sections 3 (except with
respect to the non-U.S. patents), 5.2 - 5.8, 6 and 7 of the Guarantee and
Collateral Agreement shall be of no further force and effect, and Section 8.14
of the Guarantee and Collateral Agreement shall be amended and restated in its
entirety as follows:

          "8.14 Additional Grantors.  Each Subsidiary of the Borrower that is
                -------------------
required to become a party to this Agreement pursuant to Section 9.15 of the
Note Purchase Agreement shall become a Grantor for all purposes of this
Agreement upon execution and delivery by such Subsidiary of an Assumption
Agreement in form and substance reasonably satisfactory to the Lenders."

          (b) Purchaser and/or Whitney, as applicable, shall, at the cost and
expense of the Company, (i) deliver to the Company all stock certificates and
stock powers previously delivered to Purchaser pursuant to the Pledge
Agreements, and (ii) execute and deliver to the Company such UCC-3 termination
statements and other instruments as the Company shall submit, and as are
reasonably deemed necessary or appropriate by the Company to terminate such
security interests, provided however that any of the foregoing documents
                    -------- -------
described in this Section 2.1 (collectively, the "Security Release Documents")
may be delivered to the Company after the date hereof and, in such event, the
Purchaser's and/or Whitney's, as applicable, obligation to deliver same shall
survive the closing of the transactions contemplated hereby.

                                       3
<PAGE>

     2.2  Financial Statements and Other Information.  Any requirement contained
          ------------------------------------------
in Section 8.1 or elsewhere in the Original Agreement requiring delivery by the
Company, on a weekly basis, of cash flow statements, is hereby deleted.  Section
8.1(j) of the Original Agreement is hereby deleted.

     2.3  Payment of Obligations.  Section 8.3(b) of the Original Agreement is
          ----------------------
amended and restated in its entirety as follows:

          "(b) all lawful claims which the Company and each of its Subsidiaries
is obligated to pay, which are due and which, if unpaid, might by law become a
Lien upon its property, unless the same are being contested in good faith by
appropriate proceedings and adequate reserves in accordance with GAAP are being
maintained by the Company or such Subsidiary, provided that the foregoing shall
not limit or restrict the Company's right to incur, assume or permit to exist
any Lien which constitutes a Permitted Encumbrance pursuant to Section 9.5(i) of
the Agreement."

     2.4  Limitation on Indebtedness.  Section 9.4 of the Original Agreement
          --------------------------
shall be amended and restated in its entirety as follows:

     "9.4 Limitation on Indebtedness.  Neither the Company nor any Subsidiary,
will create, incur, assume or permit to exist any Indebtedness, except
Indebtedness created under the Transaction Documents and the following
Indebtedness, in an aggregate principal amount not greater than $13,000,000 (but
such limitation of amount shall not include inter-company debt or account
balances):

          (a)  Senior Indebtedness;

          (b) Indebtedness existing on the date hereof and set forth in Schedule
9.4, and extensions, renewals and replacements of any such Indebtedness that do
not increase the outstanding principal amount thereof;

          (c) Indebtedness of the Company to any Subsidiary or of any Domestic
Subsidiary to the Company or to any other Subsidiary;

          (d) Guarantees existing on the date hereof and set forth in Schedule
9.4 by the Company of Indebtedness of any Subsidiary or by any Subsidiary of any
Indebtedness of the Company or any other Subsidiary, and extensions, renewals
and replacements of such guarantees that do not increase the outstanding amount
so guaranteed;

          (e) Indebtedness incurred to finance the acquisition, construction or
improvement of any fixed or capital assets, including Capital Lease Obligations
and any Indebtedness assumed in connection with the acquisition of any such
assets or secured by a Lien on any such assets prior to the acquisition thereof,
and extensions, renewals and replacements of any such Indebtedness that do not

                                       4
<PAGE>

increase the outstanding principal amount thereof; provided that (i) such
                                                   --------
Indebtedness is incurred prior to or within 90 days after such acquisition or
the completion of such construction or improvement and (ii) the aggregate
principal amount of Indebtedness permitted by this clause (e) shall not exceed
$300,000 at any time outstanding;

          (f) the Barclays Debt, but no extensions, renewals or replacements
thereof; and

          (g) Indebtedness in an aggregate principal amount of up to $1,200,000
to be extended after the date hereof to NMT NeuroSciences Implants (France) SA
by CIC Lyonnaise De Banque upon such terms and conditions as shall be approved
by Purchaser, which approval shall not be unreasonably withheld, and solely for
the lease of computer equipment, but no extensions, renewals or replacements
thereof.

     2.5  Limitations on Restricted Payments.  Section 9.7 of the Original
          ----------------------------------
Agreement shall be amended and restated in its entirety as follows:

     "9.7 Limitations on Restricted Payments.  The Company shall not, and shall
not permit any of its Subsidiaries to declare, or make any Restricted Payment,
except that Subsidiaries may pay dividends to the Company or any other
Subsidiary."

     2.6  Financial Covenants.  Section 9.8 of the Original Agreement shall be
          -------------------
amended and restated in its entirety as follows:

     "9.8 Financial Covenants.

          (a) Total Leverage Test.  The Company and the Subsidiaries
              -------------------
(collectively, the "Borrowers") shall not permit the ratio of the Borrowers'
consolidated Net Funded Indebtedness as of the last day of any calendar quarter
ending on the date or during any of the periods set forth below to the
Borrowers' consolidated Adjusted Operating Cash Flow for the twelve (12) month
period ending on the last day of such calendar quarter to be greater than the
ratio set forth below for such period:
<TABLE>
<CAPTION>

               Date or Period                    Ratio
               --------------                    -----
<S>                                             <C>

            September 30, 1999                  4.0:1.00

            December 31, 1999                   3.0:1.00

            January 1, 2000 and thereafter      2.5:1.00
</TABLE>

     "Net Funded Indebtedness" and "Adjusted Operating Cash Flow" will be
calculated as illustrated on Schedule 9.8.

                                       5
<PAGE>

          (b) Fixed Charge Coverage.  The Borrowers shall not permit the
              ---------------------
Borrowers' consolidated Fixed Charge Coverage for any twelve (12) month period
ending on the last day of a calendar quarter to be less than 1.50 to 1.00.

     "Fixed Charge Coverage" will be calculated as illustrated on  Schedule 9.8.

          (c) Current Ratio.  The Borrowers shall not permit the ratio of the
              -------------
Borrowers' consolidated Current Assets to the Borrowers' consolidated Current
Liabilities as of the last day of any calendar quarter to be less than 1.25 to
1.00.

     As used herein, the following terms shall have the following meanings:

     "Current Assets" shall mean, at any date, the aggregate of the current
assets of the Borrowers determined on a consolidated basis as of such date, as
determined in accordance with GAAP.

     "Current Liabilities" shall mean, at any date, the aggregate of the current
liabilities of the Borrowers, determined on a consolidated basis as of such
date, as determined in accordance with GAAP; provided, that at all times all
outstanding loans under the Credit Agreement shall be deemed to be Current
Liabilities.

          (d) Tangible Net Worth.  The Borrowers shall not permit the Borrowers'
              ------------------
Consolidated Tangible Net Worth as of the last day of any calendar quarter
during any of the periods set forth below to be less than the amount set forth
below for such period:
<TABLE>
<CAPTION>

                          Period                                Amount
                          ------                                ------
<S>                                                           <C>

   September 30, 1999 to and including December 30, 1999      $16,250,000

   December 31, 1999 to and including December 30, 2000       $17,750,000

   December 31, 2000 to and including December 30, 2001       $21,000,000

   December 31, 2001 and thereafter                           $25,000,000
</TABLE>

As used herein, the term "Consolidated Tangible Net Worth" means (a) the total
assets of the Borrowers on a consolidated basis as determined in accordance with
GAAP, minus (b) the total liabilities of the Borrowers on a consolidated basis
      -----
as determined in accordance with GAAP, minus (c) the total book value of all
                                       -----
assets of the Borrowers properly classified as intangible assets in accordance
with GAAP, including such items as good will, the purchase price of acquired
assets in excess of the fair market value thereof, trademarks, trade names,
service marks, brand names, copyrights, patents and licenses, and rights with
respect to the foregoing, minus (d) all amounts representing any write-up in the
                          -----
book value of any

                                       6
<PAGE>

assets of the Borrowers resulting from a revaluation thereof subsequent to the
date hereof, minus (e) to the extent otherwise includable in the computation of
             -----
Consolidated Tangible Net Worth, any subscriptions receivable, minus (f) all
                                                               -----
amounts representing any ownership interest in Image Technology Corp.; provided,
however, that in calculating Consolidated Tangible Net Worth no effect shall be
given to any foreign currency translations."

     2.7  Limitation on Liens.  Sections (i), (j) and (k) of Section 9.5 of the
          -------------------
Original Agreement are hereby deleted and the following is hereby included as
Section 9.5(i) thereof:

          "(i) Liens to secure Indebtedness permitted by Section 9.4, including,
without limitation, (x) Liens existing on the date hereof, all of which Liens
currently in existence are set forth on Schedule 9.5 hereto and renewals and
extensions thereof and (y) Liens otherwise permitted by Section 6.02 of the U.S.
Credit Agreement."

     2.8  Section 9.6(c) of the Original Agreement shall be amended and restated
in its entirety as follows:

     "(c) Sale and leaseback transactions relating to real estate or capital
equipment; provided however, that, subject to the Purchaser obtaining the prior
           ----------------
consent of the holders of the Senior Indebtedness, 50% of the Net Proceeds of
any such transaction shall be utilized by the Company to prepay the outstanding
principal and any outstanding interest or penalties on the New Note."

     2.9  Subsidiaries.  Section 9.15 of the Original Agreement shall be amended
          ------------
and restated in its entirety as follows:

     "9.15 Subsidiaries.

          (a)  The Company shall not, nor shall any of the Subsidiaries be
permitted to, directly or indirectly, establish, create or acquire any new
Domestic Subsidiary unless (i) such new Domestic Subsidiary shall have become a
Guarantor under the Guarantee and Collateral Agreement by executing a joinder in
form and substance satisfactory to the Purchaser, which Guarantee shall be
subordinate and junior to all Senior Indebtedness as and to the extent provided
in the New Note, and (ii) there shall have been delivered to the Purchaser such
approvals, opinions and other documents as the Purchaser may reasonably request.

          (b) With respect to any Subsidiary of the Borrower which is not a
Domestic Subsidiary (each a "Foreign Subsidiary"), the Purchaser may request any
such Foreign Subsidiary to execute a guarantee, in form and substance
satisfactory to the Purchaser, pursuant to which such Foreign Subsidiary shall
guarantee the prompt and complete payment and performance by the Company, when
due (whether at the stated maturity, acceleration or otherwise), of the
Borrower's Obligations (as defined in the Guarantee and Collateral Agreement) (a
"Foreign Guarantee"), provided that each such Foreign Guarantee
                      -------- ----

                                       7
<PAGE>

shall be limited to the amount that such Foreign Subsidiary executing such
Foreign Guarantee benefits and receives value from the Borrower Obligations (it
being intended that any such Foreign Guarantee shall be in a form which does not
create any adverse U.S. tax consequences to the Company or any Subsidiary of the
Company, in the reasonable judgment of the Company's tax advisors); and provided
                                                                        --------
further that such Foreign Guarantee shall be subordinate and junior to all
-------
Senior Indebtedness as and to the extent provided in the New Note. Each Foreign
Subsidiary executing a Foreign Guarantee shall deliver to the Purchaser such
approvals and other documents reasonably requested by the Purchaser, but no
legal or other professional opinions, provided  that the Company will not be
                                      --------  ----
required to provide any such approvals or other documents if the Company will
incur more than a minimal cost to document the same.  The Company shall not, nor
shall any of the Subsidiaries be permitted to, directly or indirectly,
establish, create or acquire any new Foreign Subsidiary unless the Company gives
the Purchaser at least ten Business Days prior written notice of the Company's
or any  Subsidiary's intention to do so."

     2.10  Notices.  Section 11.3 of the Original Agreement shall be amended and
           -------
restated in its entirety as follows:

     "11.3 Notices.  All notices, demands and other communications provided
for or permitted hereunder shall be made in writing and shall be by registered
or certified first-class mail, return receipt requested, telecopier (with
receipt confirmed), courier service or personal delivery:

           (a) if to the Purchaser:
                    Whitney Subordinated Debt Fund, L.P.
                    177 Broad Street
                    Stanford, Connecticut 06901
                    Telecopier No.: (203) 973-1422
                    Attention: Mr. Daniel J. O'Brien

               with a copy to:
                    Morrison, Cohen, Singer & Weinstein, LLP
                    750 Lexington
                    New York, New York 10022
                    Telecopier No.: (212) 735-8708
                    Attention: David A. Scherl, Esq.

           (b) if to the Company
                    NMT Medical, Inc.
                    27 Wormwood Street
                    Boston, Massachusetts 02210
                    Telecopier: (617) 737-0924
                    Attention: Mr. Theodore I. Pincus

                                       8
<PAGE>

               with a copy to:
                    Hale and Dorr, LLP
                    60 State Street
                    Boston, Massachusetts 02109
                    Telecopier: (617) 526-5000
                    Attention: Steven D. Singer, Esq.

     All such notices and communications shall be deemed to have been duly
given; when delivered by hand, if personally delivered; when delivered by
courier, if delivered by commercial overnight courier service; if mailed, five
Business Days after being deposited in the mail, postage prepaid; or if
telecopies, when receipt is acknowledged."

     2.11 Investments.  Section 9.11 of the Original Agreement is hereby amended
          -----------
to include as a permitted investment the Company's investment in ITC described
on Schedule 9.11.

                                   ARTICLE 3
                         REPRESENTATIONS AND WARRANTIES
                         ------------------------------

          The Company represents and warrants to the Purchaser as follows:

     3.1  Corporate Existence and Power.  The Company and each of its Domestic
          -----------------------------
Subsidiaries: (a) is, and after giving effect to the transactions contemplated
by this Amendment, will be a corporation duly organized, validly existing and in
good standing under the laws of the jurisdiction of its incorporation; (b) will
have all requisite corporate power and authority to own and operate its
property, to lease the property it operates as lessee and to conduct the
business in which it is currently, or is currently proposed to be, engaged; and
(c) is, and after giving effect to the transactions contemplated by this
Amendment, will be duly qualified as a foreign corporation, licensed and in good
standing under the laws of each jurisdiction where its ownership, lease or
operation of property or the conduct of its business requires such
qualification, except to the extent that the failure to do so would not have a
material adverse effect on the Condition of the Company.  The Company has the
corporate power and authority to execute, deliver and perform its obligations
under this Amendment and the New Note.

     3.2  Authority, Etc.  The execution and delivery by the Company of this
          --------------
Amendment and the performance by the Company of all of its agreements and
obligations under this Amendment and the Original Agreement as amended hereby
(i) are within the corporate authority of the Company, (ii) have been duly
authorized by all necessary corporate proceedings by the Company, (iii) do not
conflict with or result in any breach or contravention of any provision of law,
statute, rule or regulation to which the Company is subject or any judgment,
order, writ, injunction, license or permit applicable to the Company, and (iv)
do not conflict with any provision of the corporate charter or by-laws of, or
any agreement or other instrument binding upon, the Company.

                                       9
<PAGE>

     3.3  Enforceability of Obligations.  This Amendment and the Original
          -----------------------------
Agreement as amended hereby constitute the legal, valid and binding obligations
of the Company, enforceable against it in accordance with their respective
terms.

     3.4  No Default.  After giving effect to this Amendment no default or Event
          ----------
of Default exists under the New Note.


                                   ARTICLE 4
                          CONDITIONS TO EFFECTIVENESS
                          ---------------------------

          Concurrently with the execution of this Amendment:

          (a)  the Company shall deliver to the Purchaser:

               (i)   an original counterpart signature to this Amendment, duly
executed and delivered by the Company;

               (ii)  a copy of the fully-executed Credit Agreement and Guarantee
with all exhibits and schedules thereto in form and substance satisfactory to
the Purchaser;

               (iii) $14,415,110.00 by wire transfer of immediately available
funds to such account as Purchaser shall designate, in payment of $14,000,000 of
principal of the WSDF Note and all interest accrued on the WSDF Note through
September 13, 1999;

               (iv)  a Note in the principal amount of $6,000,000 (the "New
Note"), the form of which is attached hereto as Exhibit A, and
                                                ---------

               (v)   a certificate from the Company and dated the date of this
Amendment and signed by the Secretary or an Assistant Secretary of the Company,
certifying (A) that the attached copies of the Certificate of Incorporation and
By-laws of the Company, and resolutions of the Board of Directors of the
Company, approving the Transaction Documents to which it is a party and the
transactions contemplated hereby and thereby, are all true, complete and correct
and remain unamended and in full force and effect, and (B) as to the incumbency
and specimen signature of each officer of the Company executing any Transaction
Document to which it is a party or any other document delivered in connection
herewith on behalf or the Company;

          (b)  the Company shall reimburse all of the Purchaser's and Whitney's
reasonable out-of-pocket expenses, including without limitation, the reasonable
fees and disbursements of counsel, Morrison Cohen Singer & Weinstein, LLP; and

                                       10
<PAGE>

          (c)  Purchaser and Whitney, as applicable, shall deliver to the
Company:

               (i)   the WSDF Note in the original principal amount of
$20,000,000, for cancellation, and

               (ii)  the Security Release Documents to the extent required to be
delivered at such time, as provided in Section 2.1.


                                   ARTICLE 5
                                 MISCELLANEOUS
                                 -------------

     5.1  Continued Effectiveness.  Notwithstanding anything contained herein,
          -----------------------
the terms of this Amendment are not intended to and do not serve to effect a
novation as to the Original Agreement. The parties hereto expressly do not
intend to extinguish the Original Agreement. Instead, it is the express
intention of the parties hereto to reaffirm the Indebtedness created under the
Original Agreement, in the reduced amount as described herein, (including,
without limitation, the New Note) and the other documents contemplated thereby
and to reaffirm the rights and obligations contained in the Original Agreement
as amended hereby.  The Original Agreement as amended hereby and each of the
other documents contemplated thereby, as amended hereby, shall remain in full
force and effect. Except as herein amended, the Original Agreement shall remain
unchanged and in full force and effect, and is hereby ratified in all respects.
All of the representations, warranties and covenants contained in the Original
Agreement as amended hereby and in this Amendment shall survive the execution
and delivery of this Amendment.

     5.2  Successors and Assigns; Third Party Beneficiaries.  This Amendment
          -------------------------------------------------
shall inure to the benefit of and be binding upon the successors and permitted
assigns of the parties hereto. The Company may not assign any of its rights
under the Agreement without the prior written consent of the Purchaser. Except
as provided in Article 7 of the Original Agreement and in Article 7 of the New
Note, no Person other than the parties hereto and their successors and permitted
assigns is intended to be a beneficiary of any of the Transaction Documents.

     5.3  References.  Any reference to the Original Agreement contained in any
          ----------
notice, instrument, certificate, or other document executed concurrently with or
after the execution and delivery of this Amendment shall be deemed to include
the amendments contained in this Amendment unless otherwise stated therein.

     5.4  Signatures; Counterparts.  Telefacsimile transmissions of any executed
          ------------------------
original document and/or retransmission of any executed telefacsimile
transmission shall be deemed to be the same as the delivery of an executed
original. At the request of any party hereto, the other parties hereto shall
confirm telefacsimile transmissions by executing duplicate original documents
and delivering the same to the requesting party or parties. This Amendment may
be executed in any number of counterparts and by the

                                       11
<PAGE>

parties hereto in separate counterparts, each of which when so executed shall be
deemed to be an original and all of which taken together shall constitute one
and the same agreement.

     5.5  Headings.  The headings in this Amendment are for convenience of
          --------
reference only and shall not limit or otherwise affect the meaning hereof.

     5.6  GOVERNING LAW.  THIS AMENDMENT SHALL BE GOVERNED BY AND CONSTRUED IN
          -------------
ACCORDANCE WITH THE LAWS OF THE STATE OF NEW YORK, WITHOUT REGARD TO THE
PRINCIPLES OF CONFLICTS OF LAW OF SUCH STATE (INCLUDING GIVING EFFECT TO GOL
SECTION 5-1401).

     5.7  Severability.  If any one or more of the provisions contained herein,
          ------------
or the application thereof in any circumstance, is held invalid, illegal or
unenforceable in any respect for any reason, the validity, legality and
enforceability of any such provision in every other respect and of the remaining
provisions hereof shall not be in any way impaired, unless the provisions held
invalid, illegal or unenforceable shall substantially impair the benefits of the
remaining provisions hereof.

     5.8  Certain Expenses.  The Company will pay all reasonable expenses of the
          ----------------
Purchaser and of Whitney (including fees, charges and disbursements of counsel)
in connection with review, execution and delivery after the date hereof of any
of the Security Release Documents, any further amendment, supplement,
modification or waiver of or to any provision of the Agreement, the New Note,
any agency or similar agreement with respect to security interests in non-U.S.
patents requested by the Company and the holder of the Senior Indebtedness, or
any consent to any departure by the Company from the terms of any provision of
the Original Agreement as amended hereby or the New Note.


                  [REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]

                                       12
<PAGE>

          IN WITNESS WHEREOF, the parties hereto have caused this Amendment to
be executed and delivered by their respective officers hereunto duly authorized
as of the date first above written.

                         NMT MEDICAL, INC.


                         By: /s/ Thomas M. Tully
                            -------------------------
                              Name: Thomas M. Tully
                              Title: President

                         WHITNEY SUBORDINATED DEBT FUND, L.P.


                         By: /s/ Daniel J. O'Brien
                            ---------------------------
                         Name: Daniel J. O'Brien
                         A General Partner


For purposes of Sections 2.1 and 4(c) only:

                         J. H. WHITNEY & CO.


                         By: /s/ Daniel J. O'Brien
                            ---------------------------
                         Name: Daniel J. O'Brien
                         Title: General Partner



                       [signature page to amendment no.2]

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