<PAGE>   1

================================================================================

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                   FORM 10-Q

          (X) QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
                        SECURITIES EXCHANGE ACT OF 1934

                  FOR THE QUARTERLY PERIOD ENDED JUNE 30, 1999

                                       OR

          ( ) TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
                        SECURITIES EXCHANGE ACT OF 1934

     FOR THE TRANSITION PERIOD FROM                   TO

                         COMMISSION FILE NUMBER 0-18554

                       GENZYME DEVELOPMENT PARTNERS, L.P.
             (Exact name of registrant as specified in its charter)

<TABLE>
<S>                                                        <C>
                  DELAWARE                                   04-3065192
       (State or other jurisdiction of                      (IRS Employer
        incorporation or organization)                    Identification No.)

 ONE KENDALL SQUARE, CAMBRIDGE, MASSACHUSETTS                 02139-1562
   (Address of principal executive offices)                   (Zip Code)
</TABLE>

                                 (617) 252-7500
              (Registrant's telephone number, including area code)

     Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (or for such shorter period that the
registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days.  Yes  X   No ___

================================================================================
<PAGE>   2

                       GENZYME DEVELOPMENT PARTNERS, L.P.
                            FORM 10-Q, JUNE 30, 1999

                               TABLE OF CONTENTS

<TABLE>
<CAPTION>
                                                                           PAGE NO.
                                                                           --------
<S>          <C>                                                           <C>
PART I.      FINANCIAL INFORMATION
ITEM 1.      Financial Statements
             Unaudited Statements of Operations for the Three and Six          2
             Months Ended June 30, 1999 and 1998.........................
             Unaudited Balance Sheets as of June 30, 1999 and December         3
             31, 1998....................................................
             Unaudited Statements of Cash Flows for the Six Months Ended       4
             June 30, 1999 and 1998......................................
             Notes to Unaudited Financial Statements.....................      5
ITEM 2.      Management's Discussion and Analysis of Financial Condition       7
             and Results of Operations...................................
ITEM 3.      Quantitative and Qualitative Disclosures About Market             9
             Risk........................................................

PART II.     OTHER INFORMATION
ITEM 6.      Exhibits and Reports on Form 8-K............................      9
Signatures   ............................................................     10
</TABLE>

NOTE REGARDING FORWARD-LOOKING STATEMENTS:

     This Quarterly Report on Form 10-Q for Genzyme Development Partners, L.P.
(the "Partnership") contains forward-looking statements, including statements
concerning the Partnership's expected future revenues, operations and
expenditures, and the intention of Genzyme Corporation ("Genzyme") to fund the
Partnership's general and administrative expenses and research and development
programs. These forward looking statements represent the expectations of Genzyme
Development Corporation II (the "General Partner") as of the filing date of this
Form 10-Q. The Partnership's actual results could differ materially from those
anticipated by the forward looking statements due to a number of factors,
including (i) the Partnership's ability to complete successfully preclinical and
clinical development and obtain timely regulatory approval and adequate patent
and other proprietary rights protection for its products, (ii) the content and
timing of decisions made by the U.S. Food and Drug Administration ("FDA") and
other agencies regarding the Partnership's products and the indications for
which the Partnership's products may be approved, (iii) the actual size and
characteristics of markets to be addressed by the Partnership's products, (iv)
market acceptance of the Partnership's products, (v) the Partnership's ability
to obtain reimbursement for its products, (vi) the accuracy of the Partnership's
information concerning the products and resources of competitors and potential
competitors, (vii) funding of the Partnership's general and administrative
expenses and continued funding of the Partnership's research and development
programs by Genzyme, (viii) the ability of Genzyme and its subsidiaries and
Genzyme's significant suppliers, distributors, customers and partners to be Year
2000 compliant in a timely manner and (ix) the risks and uncertainties described
under the caption "Factors Affecting Future Operating Results" under Item 7.
"Management's Discussion and Analysis of Financial Condition and Results of
Operations" set forth in the Partnership's Annual Report on Form 10-K for the
fiscal year ended December 31, 1998 (the "1998 10-K").

                                        1
<PAGE>   3

                         PART I.  FINANCIAL INFORMATION

ITEM  1. FINANCIAL STATEMENTS

                       GENZYME DEVELOPMENT PARTNERS, L.P.

                            STATEMENTS OF OPERATIONS
                                  (UNAUDITED)
                      (IN THOUSANDS, EXCEPT PER UNIT DATA)

<TABLE>
<CAPTION>
                                                        THREE MONTHS ENDED    SIX MONTHS ENDED
                                                             JUNE 30,             JUNE 30,
                                                        ------------------    -----------------
                                                        1999       1998       1999      1998
                                                        -----    ---------    ----    ---------
<S>                                                     <C>      <C>          <C>     <C>
Royalty revenue from Genzyme........................    $ 44     $     19     $ 92    $      35

Costs and expenses:
     Administrative expenses........................      28           31       46           50
                                                        ----     --------     ----    ---------
Operating income (loss).............................      16          (12)      46          (15)

Equity in net loss of joint venture.................      --          (83)      --         (592)
Investment income...................................       1            1        2            1
                                                        ----     --------     ----    ---------
     Total other income (expenses)..................       1          (82)       2         (591)
                                                        ----     --------     ----    ---------
Net income (loss)...................................    $ 17     $    (94)    $ 48    $    (606)
                                                        ====     ========     ====    =========
Net income (loss) attributable to each partnership
  unit:
     Limited partners -- based on 737 units.........    $ 23     $     --     $ 65    $      --
                                                        ====     ========     ====    =========
     General partner -- based on 1 unit.............    $170     $(94,000)    $480    $(606,000)
                                                        ====     ========     ====    =========
</TABLE>

    The accompanying notes are an integral part of these unaudited financial
                                  statements.

                                        2
<PAGE>   4

                       GENZYME DEVELOPMENT PARTNERS, L.P.

                                 BALANCE SHEETS
                                  (UNAUDITED)
                                 (IN THOUSANDS)

<TABLE>
<CAPTION>
                                                                JUNE 30,    DECEMBER 31,
                                                                  1999          1998
                                                                --------    ------------
<S>                                                             <C>         <C>
                           ASSETS

Cash and cash equivalents...................................      $235          $ 97
Royalty receivable from Genzyme.............................        46            90
Investment in Joint Venture.................................        --            --
                                                                  ----          ----
          Total assets......................................      $281          $187
                                                                  ====          ====

        LIABILITIES AND PARTNERS' CAPITAL (DEFICIT)
Accrued expenses............................................      $ 48          $ 61
Payable to Genzyme..........................................       404           345
                                                                  ----          ----
          Total liabilities.................................       452           406
                                                                  ----          ----

Commitments and contingencies (Note 2)......................        --            --

Partners' capital (deficit) (including accumulated deficit
  of $34,322):
     General partner........................................      (192)         (192)
     Class A limited partners...............................        48            --
     Class B limited partners...............................        --            --
                                                                  ----          ----
                                                                  (144)         (192)
     Less: unpaid partners' capital.........................       (27)          (27)
                                                                  ----          ----
          Total partners' capital (deficit).................      (171)         (219)
                                                                  ----          ----

          Total liabilities and partners' capital
            (deficit).......................................      $281          $187
                                                                  ====          ====
</TABLE>

    The accompanying notes are an integral part of these unaudited financial
                                  statements.
                                        3
<PAGE>   5

                       GENZYME DEVELOPMENT PARTNERS, L.P.

                            STATEMENTS OF CASH FLOWS
                                  (UNAUDITED)
                                 (IN THOUSANDS)

<TABLE>
<CAPTION>
                                                                SIX MONTHS ENDED
                                                                    JUNE 30,
                                                                ----------------
                                                                1999       1998
                                                                -----     ------
<S>                                                             <C>       <C>
Cash flow from operating activities:
     Net income (loss)......................................    $ 48      $(606)
     Reconciliation of net income (loss) to net cash
      provided by operating activities:
          Equity in net loss of joint venture...............      --        592
          Increase (decrease) in cash from working capital:
               Royalties receivable from Genzyme............      44         (5)
               Payable to Genzyme and accrued expenses......      46         50
                                                                ----      -----
     Net cash provided by operating activities..............     138         31
                                                                ----      -----
Increase in cash and cash equivalents.......................     138         31
Cash and cash equivalents at beginning of period............      97         22
                                                                ----      -----
Cash and cash equivalents at end of period..................    $235      $  53
                                                                ====      =====
</TABLE>

    The accompanying notes are an integral part of these unaudited financial
                                  statements.

                                        4
<PAGE>   6

                       GENZYME DEVELOPMENT PARTNERS, L.P.
                                 JUNE 30, 1999

               NOTES TO UNAUDITED CONDENSED FINANCIAL STATEMENTS

1.  BASIS FOR PRESENTATION

     Genzyme Development Partners, L.P., a Delaware limited partnership, was
formed in September 1989 with the objective to develop, produce and derive
income from the sale of products intended to be used to limit the incidence and
severity of postoperative adhesions (the "Sepra Products"). The Sepra Products
are based on hyaluronic acid ("HA"), a naturally occurring biopolymer with
unique physical properties. In August 1996, Genzyme received marketing approval
from the FDA for the Partnership's first product, Seprafilm(R) Bioresorbable
Membrane in the U.S. on behalf of Genzyme Ventures II (the "Joint Venture"), a
joint venture between the Partnership and Genzyme.

     Per partnership unit information is based on the number of partnership
units outstanding at the end of each period. The number of units outstanding has
not changed since the date of capitalization of the Partnership.

     These unaudited financial statements should be read in conjunction with the
1998 10-K and the financial statements and footnotes included therein. Certain
information and footnote disclosures normally included in financial statements
prepared in accordance with generally accepted accounting principles have been
condensed or omitted pursuant to the rules and regulations of the Securities and
Exchange Commission.

     The financial statements for the three and six months ended June 30, 1999
and 1998 are unaudited but include, in the opinion of management, all
adjustments (consisting only of normally recurring accruals) necessary for a
fair presentation of the results for the periods presented.

2.  DEVELOPMENT AGREEMENT

     The Development Agreement calls for Genzyme to develop the Sepra Products
for the Partnership to be used as surgical aids to limit the incidence and
severity of postoperative adhesions. The Partnership was required to reimburse
Genzyme for all direct costs, a reasonable allocation of indirect costs as they
relate to the development effort and a ten percent (10%) management fee, up to
the available Partnership funds. A non-refundable retainer fee of $1.5 million
was paid by the Partnership to Genzyme when the Partnership commenced. The
General Partner, which is a wholly-owned subsidiary of Genzyme, has the
authority to terminate the research program at any time if it is deemed to be
unfeasible or uneconomical. Genzyme has no obligation to fund the research and
development programs beyond the available Partnership funds but has done so
after the available Partnership funds were expended in the first quarter of
1994. Genzyme currently intends to fund the programs through 1999 on a level
consistent with previous years and the 1999 budget for the program.

3.  JOINT VENTURE AGREEMENT

     For financial accounting purposes, Genzyme consolidates 100% of the losses
of the Joint Venture funded by its non-interest bearing loans or capital
contributions. The Partnership has not recognized losses from the Joint Venture
for the three and six months ended June 30, 1999 because its basis in the Joint
Venture was reduced to zero in 1998. For the three and six months ended June 30,
1999, the Joint Venture incurred net losses of approximately $0.1 million and
$0.6 million, respectively, and for the three and six months ended June 30,
1998, the Joint Venture incurred net losses of $1.9 million and $3.1 million,
respectively. These losses were due to the costs associated with the selling and
marketing of Seprafilm(R) Bioresorbable Membrane.

                                        5
<PAGE>   7

     Unaudited condensed financial information of the Joint Venture is
summarized below (in thousands):

<TABLE>
<CAPTION>
                                                  THREE MONTHS ENDED    SIX MONTHS ENDED
                                                       JUNE 30,             JUNE 30,
                                                  ------------------    ----------------
                                                   1999       1998       1999      1998
                                                  -------    -------    ------    ------
<S>                                               <C>        <C>        <C>       <C>
Revenues........................................  $1,751     $1,578     $3,156    $2,826
Operating expenses..............................  (1,120)    (3,015)    (2,369)   (5,207)
Net loss........................................    (134)    (1,862)      (606)   (3,134)
</TABLE>

<TABLE>
<CAPTION>
                                                               AS OF             AS OF
                                                           JUNE 30, 1999   DECEMBER 31, 1998
                                                           -------------   -----------------
<S>                                                        <C>             <C>
Venturer's capital (deficit) -- Genzyme..................      $(586)             $20
Venturer's capital -- GDP................................         --               --
</TABLE>

                                        6
<PAGE>   8

                       GENZYME DEVELOPMENT PARTNERS, L.P.
                FOR THE THREE AND SIX MONTHS ENDED JUNE 30, 1999

ITEM 2.  MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS
OF OPERATIONS

INTRODUCTION

     The following discussion is a summary of the key factors the management of
the General Partner considers necessary in reviewing the Partnership's results
of operations, liquidity and capital resources.

RESULTS OF OPERATIONS

     Net income for the three and six months ended June 30, 1999 was $17,000 and
$48,000, respectively, as compared to net losses of $94,000 and $606,000 in the
corresponding periods of 1998. The increase was primarily the result of the
absence of any loss allocation from the Joint Venture due to the reduction of
the Partnership's basis in the Joint Venture to zero during the second quarter
of 1998. Royalty revenue recognized by the Partnership on European sales of the
Sepra Products by Genzyme increased to $44,000 and $92,000 in the three and six
months ended June 30, 1999, respectively, from $19,000 and $35,000 in the same
period of 1998. Under the terms of the Cross License Agreement with Genzyme, the
Partnership is currently entitled to receive a royalty equal to 6% of net
revenues recognized from European sales of the Sepra Products to the extent
necessary to pay certain projected distributions to the partners in any year.
The General Partner believes that the Partnership will continue to be eligible
to receive such royalties during 1999.

FINANCIAL CONDITION

     As of June 30, 1999, the Partnership had $235,000 in cash and cash
equivalents, an increase of $138,000 from December 31, 1998 due primarily to the
receipt of royalty payments from Genzyme in the first and second quarter of
1999. This cash balance is reserved for general and administrative expenses.

     The Partnership's future profitability is entirely dependent upon the Joint
Venture's sales of the Sepra Products. Under the Amended and Restated Joint
Venture Agreement, Genzyme has agreed, during the term of the Joint Venture, to
make non-interest bearing loans to the Joint Venture to fund any working capital
deficiency of the Joint Venture and to make capital contributions to the extent
deemed necessary by the two venturers in connection with the business of the
Joint Venture.

     The General Partner believes that substantial additional funds will be
required to complete the development and clinical testing of the Sepra Products.
Genzyme has funded the research and development program for the Sepra Products
on an annual basis since the first quarter of 1994, when all the available funds
of the Partnership were substantially depleted. Genzyme is not obligated to fund
additional development of the Sepra Products but currently intends to continue
such funding during 1999 at a level consistent with prior years and the 1999
budget for these programs.

EURO -- THE NEW EUROPEAN CURRENCY

     All of the Partnership's revenues to date have been royalties derived from
Genzyme's European sales of Sepra Products. Since December 31, 1998, there have
been no material changes related to Genzyme's outstanding derivatives and
forward contracts or any other material contracts as a result of the Euro
conversion, nor have there been any material changes in Genzyme's or the
Partnership's competitive position as a result of the conversion. The
Partnership's disclosure related to the Euro conversion is described in the 1998
10-K under the heading "Management's Discussion and Analysis of Financial
Condition and Results of Operations -- Euro -- The New European Currency," which
is incorporated herein by reference.

YEAR 2000

     The Partnership relies upon Genzyme to provide general and administrative
and other services, and the Joint Venture relies upon Genzyme to perform
manufacturing, marketing and sales services, pursuant to certain agreements
between Genzyme, the Partnership and the Joint Venture that involve the use of

                                        7
<PAGE>   9

Genzyme's computer systems and equipment. There have been no material changes in
Genzyme's Year 2000 compliance program or its potential Year 2000 exposures
since December 31, 1998. The Partnership's disclosure related to Year 2000
issues is described in the 1998 10-K under the heading "Management's Discussion
and Analysis of Financial Condition and Results of Operations -- Year 2000,"
which is incorporated herein by reference.

                                        8
<PAGE>   10

                       GENZYME DEVELOPMENT PARTNERS, L.P.

                                   FORM 10-Q
                                 JUNE 30, 1999

ITEM 3.  QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

     Not applicable.

                          PART II.  OTHER INFORMATION

ITEM 6.  EXHIBITS AND REPORTS ON FORM 8-K

     (a) Exhibits

        27 Financial Data Schedule for Genzyme Development Partners, L.P. (for
           EDGAR filing purposes only). Filed herewith.

     (b) Reports on Form 8-K

        No reports on Form 8-K were filed during the quarter ending June 30,
        1999.

                                        9
<PAGE>   11

                       GENZYME DEVELOPMENT PARTNERS, L.P.

                                   FORM 10-Q
                                 JUNE 30, 1999

                                   SIGNATURES

     Pursuant to the requirements of the Securities Exchange Act of 1934, the
registrant has duly caused this report to be signed on its behalf by the
undersigned thereunto duly authorized.

                                            GENZYME DEVELOPMENT PARTNERS, L.P.
                                            (Registrant)

                                            By: GENZYME DEVELOPMENT CORPORATION
                                            II,
                                            its General Partner

                                            By: /s/ MICHAEL S. WYZGA

                                              ----------------------------------
                                              Michael S. Wyzga
                                              Treasurer and Chief Financial
                                                Officer

DATE: August 16, 1999

                                       10
<PAGE>   12

                       GENZYME DEVELOPMENT PARTNERS, L.P.

                                   FORM 10-Q
                                 JUNE 30, 1999

                                 EXHIBIT INDEX

<TABLE>
<CAPTION>
EXHIBIT
  NO.                              DESCRIPTION
-------                            -----------
<C>        <S>
 27        Financial Data Schedule for Genzyme Development Partners,
           L.P. (for EDGAR filing purposes only). Filed herewith.
</TABLE>