Document:

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                                                                    Exhibit 10.1

                          LOAN MODIFICATION AGREEMENT

     This LOAN MODIFICATION AGREEMENT is entered into as of December 29, 2001,
by and between SILICON VALLEY BANK, a California-chartered bank with its
principal place of business at 3003 Tasman Drive, Santa Clara, CA 95054 and with
a loan production office located at One Newton Executive Park, Suite 200, 2221
Washington Street, Newton, MA 02462, doing business under the name "Silicon
Valley East" ("Bank"), and MATRIXONE, INC., a Delaware corporation with its
principal place of business at 210 Littleton Road, Westford, MA 01886
("Borrower").

                                    RECITALS

     Borrower has borrowed money from Bank pursuant to certain Existing Loan
Documents, as defined below. In consideration of certain financial
accommodations from Bank, and Borrower's continuing obligations under the
Existing Loan Documents, Borrower and Bank agree as follows:

                                   AGREEMENT

     1.   DESCRIPTION OF EXISTING INDEBTEDNESS. Among other indebtedness which
          ------------------------------------
may be owing by Borrower to Bank, Borrower is indebted to Bank pursuant to,
among other documents, a Loan and Security Agreement dated as of December 29,
1998 between Borrower and Bank, as amended by Loan Modification Agreements dated
as of September 28, 1999, December 28, 1999, August 18, 2000, December 29, 2000,
and May 10, 2001 providing for an extension of credit up to a maximum of SEVEN
MILLION AND NO/100THS DOLLARS ($7,000,000) for working capital and equipment
finance purposes (the "Loan Agreement").

     Hereinafter, all indebtedness owing by Borrower to Bank shall be referred
to as the "Indebtedness."

     2.   DESCRIPTION OF COLLATERAL. Repayment of the Indebtedness is secured
          -------------------------
pursuant to the Loan Agreement. Hereinafter, the Loan Agreement, together with
all other documents securing payment of the Indebtedness, shall be referred to
as the "Existing Loan Documents."

     3.   DESCRIPTION OF CHANGES IN TERMS.
          -------------------------------

     3.1  Modifications to Definitions. Section 1.1 of the Loan Agreement is
          ----------------------------
hereby amended by substituting the following definitions for those set forth
therein for the same terms, and in the case of new definitions, by adding those
new definitions to that Section 1.1:

          "Committed Revolving Line" means a credit extension of up to TEN
          MILLION AND NO/100THS Dollars ($10,000,000).

          "FX Reserve" is $1,500,000

          "Revolving Maturity Date" means December 28, 2002.

          "Rights", as applied to the Collateral, means the Borrower's rights
          and interests in, and powers with respect to, that Collateral,
          whatever the nature of those rights, interests and powers and, in any
          event, including Borrower's power to transfer rights in such
          Collateral to Bank.

     3.2  Modifications to Revolving Advance Provisions. Section 2.1.1(a) of the
          ---------------------------------------------
Loan Agreement is hereby replaced in its entirety with the following:

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          (a)    Subject to and upon the terms and conditions of this Agreement,
          Bank agrees to make Advances to Borrower in an aggregate outstanding
          amount not to exceed the Committed Revolving Line or the Borrowing
          Base, whichever is less. Subject to the terms and conditions of this
          Agreement, amounts borrowed pursuant to this Section 2.1.1 may be
          repaid and reborrowed at any time during the term of this Agreement.

     3.3  Modification to Foreign Exchange Facility. Section 2.1.3 of the Loan
          -----------------------------------------
Agreement is hereby replaced in its entirety with the following:

          2.1.3  Foreign Exchange Contracts. Borrower may enter into foreign
                 --------------------------
          exchange forward contracts with the Bank under which Borrower commits
          to purchase from or sell to Bank a set amount of foreign currency more
          than one business day after the contract date (the "FX Forward
          Contract"). The total FX Forward Contracts at any one time may not
          exceed 10 times the amount of the FX Reverse. All FX Forward Contracts
          must provide for delivery or settlement on or before 90 days after the
          Revolving Maturity Date, provided that Borrower's FX Reserve
          reimbursement obligation shall be secured by cash on terms acceptable
          to Bank at any time after the Revolving Maturity Date if the term of
          this Agreement is not extended by Bank. Bank may terminate the FX
          Forward Contracts if an Event of Default occurs.

     3.4  Modifications to Overadvance Provisions.  Section 2.2. of the Loan
          ---------------------------------------
Agreement is hereby replaced in its entirety with the following:

          2.2    Overadvances. If, at any time or for any reason, the amount of
          Obligations owed by Borrower to Bank pursuant to Section 2.1.1 of this
          Agreement is greater than the lesser of (i) the Committed Revolving
          Line or (ii) the Borrowing Base, Borrower shall immediately pay to
          Bank, in cash, the amount of such excess.

     3.5  Modifications to Security Grant Provisions. Section 4.1 of the Loan
          ------------------------------------------
Agreement is hereby amended by adding the following sentence:

          Borrower authorizes Bank to file financing statements without notice
          to Borrower, with all appropriate jurisdictions, as Bank deems
          appropriate, in order to perfect or protect Bank's interest in the
          Collateral.

     3.6  Modifications to Representations and Warranties. Section 5.3 of the
          -----------------------------------------------
Loan Agreement is hereby replaced in its entirety with the following:

          5.3    Collateral. Borrower has good and indefeasible title to the
                 ----------
          Collateral, free and clear of Liens, except for Permitted Liens, or
          Borrower has Rights to each asset that is Collateral. Borrower has no
          other deposit accounts or securities accounts, other than deposit
          accounts and securities accounts with Bank and the deposit accounts
          and securities accounts described in the Schedule. The Collateral is
          not in the possession of any third party bailee (such as at a
          warehouse). If Borrower, after the date hereof, intends to store or
          otherwise deliver the Collateral to such a bailee, then Borrower must
          receive the prior written consent of Bank and such bailee must
          acknowledge in writing that the bailee is holding such Collateral for
          the benefit of Bank.

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     3.7  Modifications to Negative Covenants. Section 7.2 of the Loan Agreement
          -----------------------------------
is hereby amended by adding the following sentence:

          Borrower will not, without at least thirty (30) days prior written
          notification to Bank, reorganize, reincorporate or change its state of
          organization.

     3.8  Modifications to Borrowing Base Certificate and Compliance
          ----------------------------------------------------------
Certificate. Exhibits C and D of the Loan Agreement are hereby replaced in their
-----------
entirety with Exhibits C and D to this Agreement.

     4.   FACILTY FEE. Borrower shall pay to Bank a Loan Agreement renewal fee
          -----------
of $25,000 as well as any out-of-pocket expenses incurred by the Bank through
the date hereof, including reasonable attorneys' fees and expenses, and after
the date hereof, all Bank Expenses, including reasonable attorneys' fees and
expenses, as and when they become due.

     5.   REVISED ARTICLE 9 OF THE UCC. Borrower affirms and reaffirms that
          ----------------------------
notwithstanding the terms of the Existing Loan Documents to the contrary, (i)
that the definition of "Code" as set forth in the Existing Loan Documents shall
be deemed to mean and refer to "the Uniform Commercial Code as adopted by the
Commonwealth of Massachusetts (presently, Mass, Gen. Laws. Ch. 106), as may be
amended and in effect from time to time and (ii) the Collateral is all assets of
the Borrower (with the exception of intellectual Property, as set forth in the
Loan Agreement). In connection therewith, the Collateral shall include, without
limitation, the following categories of assets as defined in the Code: goods
(including inventory, equipment and any accessions thereto), instruments
(including promissory notes), documents, accounts (including
health-care-insurance receivables, and license fees), chattel paper (whether
tangible or electronic), deposit accounts, letter-of-credit rights (whether or
not the letter of credit is evidence by a writing), commercial tort claims,
securities and all other investment property, general intangibles (including
payment intangibles and software) but excluding intellectual Property, as set
forth in the Loan Agreement, supporting obligations and any and all proceeds of
any thereof, wherever located, whether now owned or hereafter acquired.

     6.   CONDITIONS PRECEDENT TO FURTHER ADVANCES. The obligation of Bank to
          ----------------------------------------
make further advances to Borrower under these lines is subject to the condition
precedent that Bank shall have received, in form and substance satisfactory to
Bank, the following:

          (a)  this Loan Modification Agreement duly executed by Borrower;

          (b)  payment of the fees and Bank Expenses then due specified in
Section 4 hereof; and

          (c)  such other documents, and completion of such other matters, as
Bank may reasonably deem necessary or appropriate.

     7.   CONSISTENT CHANGES. The Existing Loan Documents are hereby amended
          ------------------
wherever necessary to reflect the changes described in this Loan Modification
Agreement.

     8.   NO DEFENSES OF BORROWER. Borrower agrees that as of this date, it has
          -----------------------
no defenses against any of the obligations to pay any amounts under the
Indebtedness.

     9.   CONTINUING VALIDITY. Borrower understands and agrees that (i) in
          -------------------
modifying the Existing Loan Documents, Bank is relying upon Borrower's
representations, warranties and agreements, as set forth in the Existing Loan
Documents, (ii) except as expressly modified pursuant to this Loan Modification
Agreement (including the effects of Section 7 hereof), the Existing Loan
Documents remain unchanged and in full force and effect, (iii) Bank's agreement
to modify the Existing Loan Documents pursuant to this Loan Modification
Agreement shall in no way obligate Bank to make any future modifications to the
Existing Loan Documents, (iv) it is the intention of Bank and Borrower to retain
as

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liable parties all makers and endorsers of the Existing Loan Documents, unless a
party is expressly released by Bank in writing, (v) no maker, endorser or
guarantor will be released by virtue of this Loan Modification Agreement, and
(vi) the terms of this Section 9 apply not only to this Loan Modification
Agreement but also to all subsequent loan modification agreements, if any.

        10.     CHOICE OF LAW AND VENUE; JURY TRIAL WAIVER. The laws of the
                ------------------------------------------
Commonwealth of Massachusetts shall apply to this Agreement. BORROWER ACCEPTS
FOR ITSELF AND IN CONNECTION WITH ITS PROPERTIES, UNCONDITIONALLY, THE
NON-EXCLUSIVE JURISDICTION OF ANY STATE OR FEDERAL COURT OF COMPETENT
JURISDICTION IN THE COMMONWEALTH OF MASSACHUSETTS IN ANY ACTION, SUIT, OR
PROCEEDING OF ANY KIND AGAINST IT WHICH ARISES OUT OF OR BY REASON OF THIS
AGREEMENT; PROVIDED, HOWEVER, THAT IF FOR ANY REASON BANK CANNOT AVAIL ITSELF OF
THE COURTS OF THE COMMONWEALTH OF MASSACHUSETTS, BORROWER ACCEPTS JURISDICTION
OF THE COURTS AND VENUE IN SANTA CLARA COUNTY, CALIFORNIA. BORROWER AND BANK
EACH HEREBY WAIVE THEIR RESPECTIVE RIGHTS TO A JURY TRIAL OF ANY CLAIM OR CAUSE
OF ACTION BASED UPON OR ARISING OUT OF ANY OF THE LOAN DOCUMENTS OR ANY OF THE
TRANSACTIONS CONTEMPLATED THEREIN, INCLUDING CONTRACT CLAIMS, TORT CLAIMS,
BREACH OF DUTY CLAIMS, AND ALL OTHER COMMON LAW OR STATUTORY CLAIMS, EACH PARTY
RECOGNIZES AND AGREES THAT THE FOREGOING WAIVER CONSTITUTES A MATERIAL
INDUCEMENT FOR IT TO ENTER INTO THIS AGREEMENT. EACH PARTY REPRESENTS AND
WARRANTS THAT IT HAS REVIEWED THIS WAIVER WITH ITS LEGAL COUNSEL AND THAT IT
KNOWINGLY AND VOLUNTARILY WAIVES ITS JURY TRIAL RIGHTS FOLLOWING CONSULTATION
WITH LEGAL COUNSEL.

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

        IN WITNESS WHEREOF, the parties hereto have caused this Loan
Modification Agreement to be executed as a sealed instrument as of the date
first set forth above.

"Borrower": MATRIXONE, INC.              "Bank": SILICON VALLEY BANK, doing
                                         business as SILICON VALLEY EAST

By: /s/ Maurice Castonguay                By: /s/ Bryan Jadot
    ---------------------------              -----------------------------------
    Maurice Castonguay, CFO                  Bryan Jadot
                                             VICE PRESIDENT

                                         SILICON VALLEY BANK

                                         By: /s/ Maggie Garcia
                                             -----------------------------------

                                         Title: Loan Admin. Team Leader
                                                --------------------------------
                                         (Signed in Santa Clara County,
                                         California

                            EXHIBITS C and D FOLLOW

                                       4<PAGE>

                                                                    Exhibit 10.4

                                 AMENDMENT NO. 1

           MATRIXONE, INC. SECOND AMENDED AND RESTATED 1996 STOCK PLAN

     MatrixOne, Inc.'s Second Amended and Restated 1996 Stock Plan (the "Plan")
is hereby amended as follows:

     1.   Section 5 of the Plan is amended and restated in its entirety as
          follows:

          "Granting of Stock Rights. Stock Rights may be granted under the Plan
          at any time on or after September 30, 1996 and prior to September 30,
          2006. The date of grant of a Stock Right under the Plan will be the
          date specified by the Committee at the time it grants the Stock Right;
          provided, however, that such date shall not be prior to the date on
          which the Committee acts to approve the grant. Notwithstanding the
          preceding sentence, no Awards may be granted after January 21, 2002."

     2.   Section 6.A. of the Plan is amended and restated in its entirety as
          follows:

          "Price for Non-Qualified Options, Awards and Purchases. The exercise
          price per share specified in the agreement relating to each
          Non-Qualified Option granted under the Plan shall not be less than the
          fair market value per share of Common Stock on the date of such grant.
          The purchase price per share of stock granted in any Award or
          authorized as a Purchase under the Plan shall in no event be less than
          the minimum legal consideration required therefor under the laws of
          any jurisdiction in which the Company or its successors in interest
          may be organized."

     3.   Except as modified hereby, the Plan shall remain in full force and
          effect.

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