<PAGE>

                                                                    EXHIBIT 10.3

                                   GUARANTEE
                                   ---------

     GUARANTEE dated as of September 13, 1999 made by the guarantors which are
signatories hereto (collectively, the "Guarantors" and individually, each a
                                       ----------
"Guarantor"), in favor of BROWN BROTHERS HARRIMAN & CO. (the "Lender").
----------                                                    ------
Reference is made to that certain Credit Agreement, dated as of the date hereof
(as amended, supplemented, extended or otherwise modified from time to time, the
"French Credit Agreement"), among NMT NeuroSciences Implants (France) SA, a
 -----------------------
French limited liability company, and NMT NeuroSciences Instruments (France)
SARL, a French limited liability company (collectively, the "French
                                                             ------
Subsidiaries"), and the Lender.
------------
     WHEREAS, the French Subsidiaries have entered into the French Credit
Agreement to arrange for loans in the aggregate principal amount of 4,847,309.74
Euros (the "Loans"), the proceeds of which will be used to enable the repayment
            -----
of certain intercompany debt to one or more of the Guarantors;

     WHEREAS, pursuant to the French Credit Agreement, the Lender has agreed to
make the Loans to the French Subsidiaries upon the terms and subject to the
conditions set forth therein;

     WHEREAS, the Guarantors are direct or indirect parents or sister
subsidiaries of the French Subsidiaries;

     WHEREAS, the operations of the French Subsidiaries and the Guarantors are
conducted on a combined basis with significant shared management, purchasing,
planning, financial controls and other functions, and the French Credit
Agreement will directly or indirectly benefit the Guarantors' various
businesses; and

     WHEREAS, it is a condition precedent to the obligations of the Lender to
make the Loans to the French Subsidiaries under the French Credit Agreement that
the Guarantors shall have executed and delivered this Guarantee to the Lender.

     NOW, THEREFORE, in consideration of the premises and to induce the Lender
to enter into the French Credit Agreement and to make the Loans to the French
Subsidiaries under the French Credit Agreement, each Guarantor hereby agrees
with the Lender as follows:

     1.   Defined Terms.  Capitalized terms not otherwise defined herein shall
          -------------
have the meanings set forth in the French Credit Agreement.

     2.   Guarantee.
          ---------

          (a) Each Guarantor hereby jointly and severally, unconditionally and
irrevocably, guarantees to the Lender and its respective successors, endorsees,
transferees and assigns, the prompt and complete payment and performance by the
French Subsidiaries when due (whether at the stated
<PAGE>

maturity, by acceleration or otherwise) of the unpaid principal of and interest
on the Loans and all other obligations and liabilities of the French
Subsidiaries to the Lender (including interest accruing at the then applicable
rate provided in the French Credit Agreement after the stated maturity, by
acceleration or otherwise), whether direct or indirect, absolute or contingent,
due or to become due, now existing or hereafter incurred, which may arise under,
out of, or in connection with, the French Credit Agreement or any other document
made, delivered or given in connection therewith, whether on account of
principal, interest, fees, indemnities, costs, expenses or otherwise (including
all reasonable fees and disbursements of counsel to the Lender that are required
to be paid by the French Subsidiaries pursuant to the terms of the French Credit
Agreement) (each and all of the above obligations, collectively, the "Guaranteed
                                                                      ----------
Obligations").
-----------

          (b) Each Guarantor further agrees to pay any and all expenses
(including all reasonable fees and disbursements of counsel) which may be paid
or incurred by the Lender in enforcing any rights with respect to, or collecting
against, any Guarantor under this Guarantee.  This Guarantee shall remain in
full force and effect until the Guaranteed Obligations and all amounts owing
hereunder are paid in full and any obligations to provide financial
accommodations to the French Subsidiaries under the French Credit Agreement are
terminated.

          (c) No payment or payments made by any French Subsidiary, any
Guarantor or any other Person or received or collected by the Lender from any
French Subsidiary, any Guarantor or any other Person by virtue of any action or
proceeding or any set-off or appropriation or application at any time or from
time to time in reduction of or in payment of any Guaranteed Obligations shall
be deemed to modify, reduce, release or otherwise affect the liability of any
Guarantor hereunder which shall, notwithstanding any such payment or payments,
remain liable for the Guaranteed Obligations until the Guaranteed Obligations
and all amounts owing hereunder are paid in full and any obligations to provide
financial accommodations to the French Subsidiaries under the French Credit
Agreement are terminated.

     3.   Right of Set-off.  In addition to any rights now or hereafter granted
          ----------------
under applicable law or otherwise, and not by way of limitation of any such
rights, upon the occurrence and during the continuance of an Event of Default,
the Lender is hereby authorized at any time or from time to time, without
presentment, demand, protest or other notice of any kind to the French
Subsidiaries, any Guarantor or to any other Person, any such notice being hereby
expressly waived, to set off and to appropriate and apply any and all deposits
(general or special, but excluding any deposits in payroll or escrow accounts)
and any other Indebtedness at any time held or owing by the Lender (including,
without limitation, by branches and agencies of the Lender wherever located) to
or for the credit or the account of any Guarantor against and on account of the
obligations and liabilities of any Guarantor hereunder, and all other claims of
any nature or description arising out of or connected with this Guarantee,
irrespective of whether the Lender shall have made any demand hereunder and
although said obligations, liabilities or claims, or any of them, shall be
contingent or unmatured.

     4.   No Subrogation.  Notwithstanding any payment or payments made by any
          --------------
Guarantor hereunder or any set-off or application of funds of any Guarantor by
the Lender, no Guarantor shall be

                                       2
<PAGE>

entitled to exercise or enforce any subrogation rights of the Lender against the
French Subsidiaries or any other Person or any guarantee or right of offset held
by the Lender for the payment of the Guaranteed Obligations, nor shall any
Guarantor seek or be entitled to seek any contribution or reimbursement from the
French Subsidiaries or any other Person in respect of payments made by any
Guarantor hereunder, until all amounts owing to the Lender by the French
Subsidiaries on account of the Guaranteed Obligations and all amounts owing
hereunder are paid in full and any obligations to provide financial
accommodations to the French Subsidiaries under the French Credit Agreement are
terminated. If any amount shall be paid to any Guarantor on account of such
subrogation rights at any time when all of the Guaranteed Obligations and all
amounts owing hereunder shall not have been paid in full or any obligations to
provide financial accommodations to the French Subsidiaries under the French
Credit Agreement shall not have been terminated, such amount shall be held by
such Guarantor in trust for the Lender, segregated from other funds of such
Guarantor, and shall, forthwith upon receipt by such Guarantor, be turned over
to the Lender in the exact form received by such Guarantor (duly indorsed by
such Guarantor to the Lender, if required), to be applied against such
Guaranteed Obligations, whether matured or unmatured, in such order as the
Lender may determine.

     5.   Amendments, etc. with respect to the Guaranteed Obligations; Waiver of
          ----------------------------------------------------------------------
Rights.  Each Guarantor shall remain obligated hereunder notwithstanding that,
------
without any reservation of rights against such Guarantor and without notice to
or further assent by such Guarantor, any demand for payment of any of the
Guaranteed Obligations made by the Lender may be rescinded by such party and any
of the Guaranteed Obligations continued, and the Guaranteed Obligations, or the
liability of any other party upon or for any part thereof, or any guarantee
therefor or right of offset with respect thereto, may, from time to time, in
whole or in part, be renewed, extended, amended, modified, accelerated,
compromised, waived, surrendered or released by the Lender, and the French
Credit Agreement may be amended, modified, supplemented or terminated, in whole
or in part, as the Lender may deem advisable from time to time, and any
guarantee or right of offset at any time held by the Lender for the payment of
the Guaranteed Obligations may be waived.  When making any demand hereunder
against any Guarantor, the Lender may, but shall be under no obligation to, make
a similar demand on the French Subsidiaries or any other Guarantor, and any
failure by the Lender to make any such demand or to collect any payments from
the French Subsidiaries or any other Guarantor or any release of the French
Subsidiaries or such other Guarantor shall not relieve any Guarantor, and shall
not impair or affect the rights and remedies, express or implied, or as a matter
of law, of the Lender against any Guarantor.  For the purposes hereof "demand"
shall include the commencement and continuance of any legal proceedings.

     6.   Guarantee Absolute and Unconditional.  Each Guarantor waives any and
          ------------------------------------
all notice of the creation, renewal, extension or accrual of any of the
Guaranteed Obligations and notice of or proof of reliance by the Lender upon
this Guarantee or acceptance of this Guarantee; the Guaranteed Obligations, and
any of them, shall conclusively be deemed to have been created, contracted or
incurred, or renewed, extended, amended or waived, in reliance upon this
Guarantee; and all dealings between the French Subsidiaries and each Guarantor,
on the one hand, and the Lender, on the other hand, likewise shall be
conclusively presumed to have been had or consummated in reliance upon this
Guarantee.  Each Guarantor waives diligence, presentment, protest, demand for
payment and notice of

                                       3
<PAGE>

default or nonpayment to or upon the French Subsidiaries or such Guarantor with
respect to the Guaranteed Obligations. Each Guarantor understands and agrees
that this Guarantee shall be construed as a continuing, absolute and
unconditional guarantee and surety of payment without regard to (a) the
validity, regularity or enforceability of the French Credit Agreement, any of
the Guaranteed Obligations or any other guarantee or right of offset with
respect thereto at any time or from time to time held by the Lender, (b) any
defense, set-off or counterclaim (other than a defense of payment or
performance) which may at any time be available to or be asserted by the French
Subsidiaries or any Guarantor against the Lender, or (c) any other circumstance
whatsoever (with or without notice to or knowledge of the French Subsidiaries or
any Guarantor) which constitutes, or might be construed to constitute, an
equitable or legal discharge of any French Subsidiary for the Guaranteed
Obligations, or of any Guarantor under this Guarantee, in bankruptcy or in any
other instance. When pursuing its rights and remedies hereunder against any
Guarantor, the Lender may, but shall be under no obligation to, pursue such
rights and remedies as it may have against the French Subsidiaries or any other
Person or against any guarantee for the Guaranteed Obligations or any right of
offset with respect thereto, and any failure by the Lender to pursue such other
rights or remedies or to collect any payments from the French Subsidiaries or
any such other Person or to realize upon any guarantee or to exercise any such
right of offset, or any release of the French Subsidiaries or any such other
Person or any such guarantee or right of offset, shall not relieve any Guarantor
of any liability hereunder, and shall not impair or affect the rights and
remedies, whether express, implied or available as a matter of law, of the
Lender against any Guarantor. This Guarantee shall remain in full force and
effect and be binding in accordance with and to the extent of its terms upon
each Guarantor and the successors and assigns thereof, and shall inure to the
benefit of the Lender, and its respective successors, endorsees, transferees and
assigns, until all the Guaranteed Obligations and the obligations of each
Guarantor under this Guarantee shall have been satisfied by payment in full and
any obligations to provide financial accommodations to the French Subsidiaries
under the French Credit Agreement shall have been terminated.

     7.   Reinstatement.  This Guarantee shall continue to be effective, or be
          -------------
reinstated, as the case may be, if at any time payment, or any part thereof, of
any of the Guaranteed Obligations is rescinded or must otherwise be restored or
returned by the Lender upon the insolvency, bankruptcy, dissolution, liquidation
or reorganization of any French Subsidiary or Guarantor, or upon or as a result
of the appointment of a receiver, intervenor or conservator of, or trustee or
similar officer for, any French Subsidiary or Guarantor or any substantial part
of its property, or otherwise, all as though such payments had not been made.

     8.   Payments.  Each Guarantor hereby guarantees that payments made by such
          --------
Guarantor of principal of and interest on the Loans pursuant to the terms hereof
(such payments to be made in Euros) and any other payments hereunder (such
payments to be made in U.S. dollars) will be made to the Lender without set-off
or counterclaim at the office of the Lender located at 40 Water Street, Boston,
MA 02109-3661.

     9.   Representations and Warranties.  In order to induce the Lender to
          ------------------------------
enter into the French Credit Agreement and to make the Loans to the French
Subsidiaries thereunder, each Guarantor hereby represents and warrants to the
Lender that the respective representations and warranties of such

                                       4
<PAGE>

Guarantor set forth in Article III of that certain Credit Agreement, dated as of
the date hereof, by and among the Guarantors and the Lender (the "U.S. Credit
                                                                  -----------
Agreement") (each Guarantor in such capacity, a "Borrower") are true and
---------
correct.

     10.  Compliance with U.S. Credit Agreement.
          -------------------------------------

          (a) In order to induce the Lender to enter into the French Credit
Agreement and to make the Loans to the French Subsidiaries thereunder, until all
amounts owing to the Lender by the French Subsidiaries on account of the
Guaranteed Obligations and all amounts owing hereunder are paid in full and any
obligations to provide financial accommodations to the French Subsidiaries under
the French Credit Agreement are terminated, each Guarantor covenants and agrees
with the Lender to, at all times, observe and perform, or cause to be observed
and performed, all of the covenants, conditions and obligations required to be
observed and performed, or caused to be observed and performed, by such
Guarantor under the U.S. Credit Agreement, including, without limitation, the
affirmative and negative covenants set forth in Articles V and VI thereof.

          (b) At any time upon the request of the Lender, to the extent
permitted by applicable law, the Guarantors will, within a reasonable period
after such request, cause any Subsidiary (as defined in the U.S. Credit
Agreement) that is not a Domestic Subsidiary (as defined in the U.S. Credit
Agreement) to become a party hereto or otherwise guarantee the Guaranteed
Obligations, in form and substance satisfactory to the Lender; provided that
                                                               --------
such guarantee shall be limited in amount and otherwise in a form which does not
create any adverse U.S. tax consequences to the Guarantors in the reasonable
judgment of the Guarantors' tax advisors.

     11.  Notice.  All notices and other communications provided for herein
          ------
shall be in writing and shall be delivered by hand or overnight courier service,
mailed by certified or registered mail or sent by telecopy, as follows:

          (a) if to any Guarantor, to it at 27 Wormwood Street, Boston,
Massachusetts 02210-1625, Attention of Chief Financial Officer (Telecopy No.
617-737-0924), with a copy to Hale and Dorr LLP, 60 State Street, Boston,
Massachusetts 02109, Attention of Steven D. Singer, Esq. (Telecopy No. 617-526-
5000); and

          (b) if to the Lender, to Brown Brothers Harriman & Co., 40 Water
Street, Boston, Massachusetts 02109-3661, Attention of Victoria W. Evans,
Assistant Manager (Telecopy No. 617-772-1138), with a copy to Goodwin, Procter &
Hoar LLP, Exchange Place, Boston, Massachusetts 02109-2881, Attention of Raymond
C. Zemlin, P.C. (Telecopy No. 617-523-1231);

Any party hereto may change its address or telecopy number for notices and other
communications hereunder by notice to the other parties hereto.  All notices and
other communications given to any party hereto in accordance with the provisions
of this Guarantee shall be deemed to have been given on the date of receipt.

                                       5
<PAGE>

     12.  Severability.  Any provision of this Guarantee which is prohibited or
          ------------
unenforceable in any jurisdiction shall, as to such jurisdiction, be ineffective
to the extent of such prohibition or unenforceability without invalidating the
remaining provisions hereof, and any such prohibition or unenforceability in any
jurisdiction shall not invalidate or render unenforceable such provision in any
other jurisdiction.

     13.  Integration.  This Guarantee and the documents referred to herein
          -----------
represent the entire agreement of the Guarantors with respect to the subject
matter hereof and there are no promises or representations by the Lender
relative to the subject matter hereof not reflected herein or therein.

     14.  Amendments in Writing; No Waiver; Cumulative Remedies.
          -----------------------------------------------------

          (a)  None of the terms or provisions of this Guarantee may be waived,
amended, supplemented or otherwise modified except as provided in Section 7.02
of the French Credit Agreement.

          (b) The Lender shall not by any act (except by a written instrument
pursuant to Section 14(a) hereof), delay, indulgence, omission or otherwise be
deemed to have waived any right or remedy hereunder or to have acquiesced in any
Default or Event of Default or in any breach of any of the terms and conditions
hereof.  No failure to exercise, nor any delay in exercising, on the part of the
Lender any right, power or privilege hereunder shall operate as a waiver
thereof.  No single or partial exercise of any right, power or privilege
hereunder shall preclude any other or further exercise thereof or the exercise
of any other right, power or privilege.  A waiver by the Lender of any right or
remedy hereunder on any one occasion shall not be construed as a bar to any
right or remedy which the Lender would otherwise have on any future occasion.

          (c) The rights and remedies herein provided are cumulative, may be
exercised singly or concurrently and are not exclusive of any other rights or
remedies provided by law.

     15.  Section Headings.  The section headings used in this Guarantee are for
          ----------------
convenience of reference only and are not to affect the construction hereof or
be taken into consideration in the interpretation hereof.

     16.  Successors and Assigns.  This Guarantee shall be binding upon the
          ----------------------
successors and assigns of each Guarantor and shall inure to the benefit of the
Lender and its successors and assigns.

     17.  Governing Law; Jurisdiction; Consent to Service of Process.
          ----------------------------------------------------------

          (a)  This Guarantee shall be construed in accordance with and governed
by the law of the Commonwealth of Massachusetts.

          (b)  Each of the Guarantors hereby irrevocably and unconditionally
submits, for itself and its property, to the nonexclusive jurisdiction of the
Superior Court of the Commonwealth of

                                       6
<PAGE>

Massachusetts sitting in Suffolk County and of the United States District Court
for the District of Massachusetts, and any appellate court from any thereof, in
any action or proceeding arising out of or relating to this Guarantee, or for
recognition or enforcement of any judgment, and each of the parties hereto
hereby irrevocably and unconditionally agrees that all claims in respect of any
such action or proceeding may be heard and determined in such Commonwealth of
Massachusetts or, to the extent permitted by law, such Federal court. Each of
the parties hereto agrees that a final judgment in any such action or proceeding
shall be conclusive and may be enforced in other jurisdictions by suit on the
judgment or in any other manner provided by law. Nothing in this Guarantee shall
affect any right that the Lender may otherwise have to bring any action or
proceeding relating to this Guarantee against any Guarantor or its properties in
the courts of any jurisdiction.

          (c) Each Guarantor hereby irrevocably and unconditionally waives, to
the fullest extent it may legally and effectively do so, any objection which it
may now or hereafter have to the laying of venue of any suit, action or
proceeding arising out of or relating to this Guarantee in any court referred to
in paragraph (b) of this Section.  Each of the parties hereto hereby irrevocably
waives, to the fullest extent permitted by law, the defense of an inconvenient
forum to the maintenance of such action or proceeding in any such court.

          (d) Each Guarantor hereby agrees that service of all writs,
complaints, process and summonses in any suit, action or proceeding arising out
of or relating to this Guarantee, or for recognition or enforcement of any
judgment, may be made upon NMT Medical, Inc., a Delaware corporation (the
"Process Agent"), with an office on the date hereof at 27 Wormwood Street,
--------------
Boston, Massachusetts 02210-1625.  Each Guarantor hereby irrevocably appoints
the Process Agent its true and lawful attorney-in-fact in its name, place and
stead to accept such service of any and all such writs, complaints, process and
summonses.  Each Guarantor agrees that any election by the Lender to give notice
of any such service to such Guarantor shall not impair or affect the validity of
such service or of the judgment based thereon.

          (e) Each party to this Guarantee irrevocably consents to service of
process in the manner provided for notices in Section 11.  Nothing in this
Guarantee will affect the right of any party to this Guarantee to serve process
in any other manner permitted by law.

     18.    WAIVER OF JURY TRIAL.  EACH PARTY HERETO HEREBY WAIVES, TO THE
            --------------------
FULLEST EXTENT PERMITTED BY APPLICABLE LAW, ANY RIGHT IT MAY HAVE TO A TRIAL BY
JURY IN ANY LEGAL PROCEEDING DIRECTLY OR INDIRECTLY ARISING OUT OF OR RELATING
TO THIS GUARANTEE OR THE TRANSACTIONS CONTEMPLATED HEREBY (WHETHER BASED ON
CONTRACT, TORT OR ANY OTHER THEORY).  EACH PARTY HERETO (A) CERTIFIES THAT NO
REPRESENTATIVE, AGENT OR ATTORNEY OF ANY OTHER PARTY HAS REPRESENTED, EXPRESSLY
OR OTHERWISE, THAT SUCH OTHER PARTY WOULD NOT, IN THE EVENT OF LITIGATION, SEEK
TO ENFORCE THE FOREGOING WAIVER AND (B) ACKNOWLEDGES THAT IT AND THE OTHER
PARTIES HERETO HAVE BEEN INDUCED

                                       7
<PAGE>

TO ENTER INTO THIS GUARANTEE BY, AMONG OTHER THINGS, THE MUTUAL WAIVERS AND
CERTIFICATIONS IN THIS SECTION.

     19.  No Offset.  All payments by the Guarantors hereunder shall be made
          ---------
without setoff or counterclaim and free and clear of and without deduction for
any foreign or domestic taxes, levies, imposts, duties, charges, fees,
deductions, withholdings, compulsory loans, restriction or conditions of any
nature now or hereafter imposed or levied by any jurisdiction or any political
subdivision thereof or taxing or other authority therein unless any Guarantor is
required by law to make such deduction or withholding.  Except as otherwise
expressly provided in this Section 19, if any such obligation is imposed upon
any Guarantor with respect to any amount payable hereunder, such Guarantor will
pay to the Lender, on the date on which such amount is due and payable
hereunder, such additional amount as shall be necessary to enable the Lender to
receive the same net amount which it would have received on such due date had no
such obligation been imposed upon such Guarantor.  The Guarantors will deliver
promptly to the Lender, certificates or other valid vouchers for all taxes or
other charges deducted from or paid with respect to payments made by the
Guarantors hereunder.

     20.  Senior Status of Obligations.  All rights of the Lender with respect
          ----------------------------
to the payment and performance of all Guaranteed Obligations by the Guarantors
hereunder of every kind and description, whether now existing or hereafter
arising, shall be senior to all rights of the holders of the Whitney Notes, and
such rights of the Lender shall not be subordinated in right of payment to any
other Indebtedness of any Guarantor.

                  [REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]

                                       8
<PAGE>

     IN WITNESS WHEREOF, each of the undersigned has caused this Guarantee to be
duly executed and delivered by its duly authorized officer as of the day and
year first above written.

                                    NMT MEDICAL, INC.


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


                                    NMT HEART, INC.


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


                                    NMT INVESTMENTS CORP.


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


                                    NMT NEUROSCIENCES
                                    (INTERNATIONAL), INC.


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


                                    NMT NEUROSCIENCES (US), INC.


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

                                       9
<PAGE>

                                    NMT NEUROSCIENCES (IP), INC.


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


                                    NMT NEUROSCIENCES
                                    INNOVASIVE SYSTEMS, INC.


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

                                       10