<PAGE>   1

                       SECURITIES AND EXCHANGE COMMISSION

                             WASHINGTON, D.C. 20549

                                   FORM 10-K/A

              ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE

                         SECURITIES EXCHANGE ACT OF 1934

                   FOR THE FISCAL YEAR ENDED DECEMBER 31, 1999

                         COMMISSION FILE NUMBER 0-26872

                          GELTEX PHARMACEUTICALS, INC.
             (Exact Name of Registrant as Specified in its Charter)
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<S>                                                         <C>
               Delaware                                        04-3136767
    (State or other jurisdiction of                         (I.R.S. Employer
     Incorporation or organization)                        Identification No.)

           153 Second Avenue
         Waltham, Massachusetts                                  02451
(Address of principal executive offices)                       (Zip Code)
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       REGISTRANT'S TELEPHONE NUMBER, INCLUDING AREA CODE: (781) 290-5888

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<S>                                                                <C>
Securities registered pursuant to Section 12(b) of the Act:        None

Securities registered pursuant to Section 12(g) of the Act:        Common Stock, $.01 par value per share
                                                                   Junior Participating Preferred Stock
                                                                   Purchase Rights

                                                                   (Title of Class)
</TABLE>

    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

    Indicate by check mark if disclosure of delinquent filers pursuant to Item
405 of Regulation S-K is not contained herein, and will not be contained, to the
best of registrant's knowledge, in definitive proxy or information statements
incorporated by reference in Part III of this Form 10-K or any amendment to this
Form 10-K. [ ]

    The aggregate market value, based upon the closing sale price of the shares
as reported by The Nasdaq Stock Market(R), of voting stock held by
non-affiliates (without admitting that any person whose shares are not included
in such calculation is an affiliate) at March 23, 2000 was $387,627,880.

    As of March 23, 2000, 19,817,006 shares of the registrant's Common Stock,
$.01 par value per share, were issued and outstanding.

                       DOCUMENTS INCORPORATED BY REFERENCE
   PORTIONS OF THE REGISTRANT'S DEFINITIVE PROXY STATEMENT FOR ITS 2000 ANNUAL
                   MEETING OF STOCKHOLDERS ARE INCORPORATED BY
              REFERENCE INTO PART III OF THIS REPORT ON FORM 10-K.

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     This Annual Report on Form 10-K/A constitutes Amendment No. 1 to the
Registrant's Form 10-K for the fiscal year ended December 31, 1999.

     The Exhibit Index referred to in Item 14 is hereby amended to add the
following exhibits:

     -  Exhibit 10.33, GT 102-279 Collaboration Agreement between the
        Registrant and Sankyo Pharma, Inc. dated as of December 23, 1999.

     -  Exhibit 10.34, Collaboration Agreement between the Registrant and Sankyo
        Pharma, Inc. dated as of December 23, 1999

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                                   SIGNATURES

    Pursuant to the requirements of Section 13 or Section 15(d) of the
Securities Exchange Act of 1934, the Company has duly caused this report to be
signed on its behalf by the undersigned, thereunto duly authorized.


                                            GELTEX PHARMACEUTICALS, INC.



Date: November 6, 2000                      By:    /s/ Mark Skaletsky
                                                 -------------------------------
                                                 Mark Skaletsky
                                                 President and Chief Executive
                                                 Officer


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                                  EXHIBIT INDEX

*4.1         First Amendment to Rights Agreement between GelTex Pharmaceuticals,
             Inc. and American Stock Transfer and Trust Company, dated as of
             July 29, 1997. Filed as Exhibit 4.3 to GelTex Pharmaceuticals,
             Inc.'s Quarterly Report on Form 10-Q for the quarter ended June 30,
             1997 and incorporated herein by reference.

*4.2         Amended and Restated Facility One Term Note issued by GelTex
             Pharmaceuticals, Inc. to Fleet National Bank, dated as of May 21,
             1997. Filed as Exhibit 4.1 to GelTex Pharmaceuticals, Inc.'s
             Quarterly Report on Form 10-Q for the quarter ended June 30, 1998
             and incorporated herein by reference.

*4.3         Security Agreement (Equipment) between GelTex Pharmaceuticals, Inc.
             and Fleet National Bank, dated May 21, 1997. Filed as Exhibit 4.4
             to GelTex Pharmaceuticals, Inc.'s Registration Statement on
             Form S-3 (No. 333-45151) and incorporated herein by reference.

*4.4         Letter Agreement between GelTex Pharmaceuticals, Inc. and Fleet
             National Bank, dated May 21, 1997. Filed as Exhibit 4.5 to GelTex
             Pharmaceuticals, Inc.'s Registration Statement on Form S-3 (No.
             333-45151) and incorporated herein by reference.

*4.5         Promissory Note, dated October 31, 1997, issued by GelTex
             Pharmaceuticals, Inc. to Fleet National Bank. Filed as Exhibit 4.6
             to GelTex Pharmaceuticals, Inc.'s Registration Statement on Form
             S-3 (No. 333-45151) and incorporated herein by reference.

*4.6         Loan Modification Agreement between GelTex Pharmaceuticals, Inc.
             and Fleet National Bank, dated October 31, 1997. Filed as Exhibit
             4.7 to GelTex Pharmaceuticals, Inc.'s Registration Statement on
             Form S-3 (No. 333-45151) and incorporated herein by reference.

*4.7         Second Loan Modification Agreement between GelTex Pharmaceuticals,
             Inc. and Fleet National Bank, dated as of June 30, 1998. Filed as
             Exhibit 4.2 to GelTex Pharmaceuticals, Inc.'s Quarterly Report on
             Form 10-Q for the quarter ended June 30, 1998 and incorporated
             herein by reference.

*4.8         Letter Agreement between GelTex Pharmaceuticals, Inc. and Fleet
             National Bank dated October 4, 1999. Filed as Exhibit 4.1 to GelTex
             Pharmaceuticals, Inc.'s Quarterly Report on Form 10-Q for the
             quarter ended September 30, 1999 and incorporated herein by
             reference.

*4.9         Promissory Note, dated October 4, 1999, issued by GelTex
             Pharmaceuticals, Inc. to Fleet National Bank. Filed as Exhibit 4.2
             to GelTex Pharmaceuticals, Inc.'s Quarterly Report on Form 10-Q for
             the quarter ended September 30, 1999 and incorporated herein by
             reference.

*10.1#       GelTex Pharmaceuticals, Inc. Amended and Restated 1992 Equity
             Incentive Plan. Filed as Exhibit 10.1 to GelTex Pharmaceuticals,
             Inc.'s Quarterly Report on Form 10-Q for the quarter ended June 30,
             1999 and incorporated herein by reference.

*10.2**      License Agreement between GelTex Pharmaceuticals, Inc. and Chugai
             Pharmaceutical Co., Ltd., dated December 26, 1994. Filed as Exhibit
             10.14 to GelTex Pharmaceuticals, Inc.'s Registration Statement on
             Form S-1 (File No. 33-97322) and incorporated herein by reference.

*10.3        Form of Common Stock Purchase Agreement. Filed as Exhibit 10.17 to
             GelTex Pharmaceuticals, Inc.'s Registration Statement on Form S-1
             (File No. 33-97322) and incorporated herein by reference.

*10.4        Form of Restricted Common Stock Purchase Agreement. Filed as
             Exhibit 10.18 to GelTex Pharmaceuticals, Inc.'s Registration
             Statement on Form S-1 (File No. 33-97322) and incorporated herein
             by reference.

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*10.5#       Form of Incentive Stock Option Certificate. Filed as Exhibit 10.19
             to GelTex Pharmaceuticals, Inc.'s Registration Statement on Form
             S-1 (File No. 33-97322) and incorporated herein by reference.

*10.6#       Form of Nonstatutory Stock Option Certificate. Filed as Exhibit
             10.20 to GelTex Pharmaceuticals, Inc.'s Registration Statement on
             Form S-1 (File No. 33-97322) and incorporated herein by reference.

*10.7#       GelTex Pharmaceuticals, Inc. Amended and Restated 1995 Director
             Stock Option Plan. Filed as Exhibit 10.2 to GelTex Pharmaceuticals,
             Inc.'s Quarterly Report on Form 10-Q for the quarter ended June 30,
             1999 and incorporated herein by reference.

*10.8#       GelTex Pharmaceuticals, Inc. 1995 Employee Stock Purchase Plan.
             Filed as Exhibit 99.1 to GelTex Pharmaceuticals, Inc.'s
             Registration Statement on Form S-8 (File No. 333-00864) and
             incorporated herein by reference.

*10.9        Lease Agreement dated February 28, 1997, between GelTex
             Pharmaceuticals, Inc. and J.F. White Properties, Inc. Filed as
             Exhibit 10.16 to GelTex Pharmaceuticals, Inc.'s Annual Report on
             Form 10-K for the year ended December 31, 1996.

*10.10**     Contract Manufacturing Agreement between GelTex Pharmaceuticals,
             Inc. and The Dow Chemical Company. Filed as Exhibit 10.17 to GelTex
             Pharmaceuticals, Inc.'s Quarterly Report on Form 10-Q for the
             quarter ended March 31, 1997 and incorporated herein by reference.

*10.11**     Collaboration Agreement among GelTex Pharmaceuticals, Inc.,
             Genzyme Corporation and RenaGel LLC dated as of June 17, 1997.
             Filed as Exhibit 10.18 to GelTex Pharmaceuticals, Inc.'s Quarterly
             Report on Form 10-Q for the quarter ended June 30, 1997 and
             incorporated herein by reference

*10.12       Purchase Agreement between GelTex Pharmaceuticals, Inc. and Genzyme
             Corporation, dated as of June 17, 1997. Filed as Exhibit 10.19 to
             GelTex Pharmaceuticals, Inc.'s Quarterly Report on Form 10-Q for
             the quarter ended June 30, 1997 and incorporated herein by
             reference.

*10.13**     Operating Agreement of RenaGel LLC, dated as of June 17, 1997.
             Filed as Exhibit 10.20 to GelTex Pharmaceuticals, Inc.'s Quarterly
             Report on Form 10-Q for the quarter ended June 30, 1997 and
             incorporated herein by reference.

*10.14**     License Agreement between GelTex Pharmaceuticals, Inc. and Nitto
             Boseki Co., Ltd., dated as of June 9, 1997. Filed as Exhibit 10.21
             to GelTex Pharmaceuticals, Inc.'s Quarterly Report on Form 10-Q for
             the quarter ended June 30, 1997 and incorporated herein by
             reference.

*10.15#      Letter Agreement between GelTex Pharmaceuticals, Inc. and Paul J.
             Mellett, Jr., dated March 11, 1997. Filed as Exhibit 10.19 to
             GelTex Pharmaceuticals, Inc.'s Annual Report on Form 10-K for the
             year ended 1997 and incorporated herein by reference.

*10.16#      Letter Agreement between GelTex Pharmaceuticals, Inc. and Edmund J.
             Sybertz, Jr., dated November 17, 1997. Filed as Exhibit 10.20 to
             GelTex Pharmaceuticals, Inc.'s Annual Report on Form 10-K for the
             year ended 1997 and incorporated herein by reference.

*10.17#      Promissory Note in favor of GelTex Pharmaceuticals, Inc. executed
             by Edmund J. Sybertz, Jr., dated June 30, 1998. Filed as Exhibit
             10.3 to GelTex Pharmaceuticals, Inc.'s Quarterly Report on Form
             10-Q for the quarter ended June 30, 1998 and incorporated herein by
             reference.

*10.18       Purchase and Sale Agreement between Sodexho USA, Inc., Service
             Supply Corporation and GelTex Pharmaceuticals, Inc., dated as of
             August 4, 1998. Filed as Exhibit 10.5 to GelTex Pharmaceuticals,
             Inc.'s Quarterly Report on Form 10-Q for the quarter ended June 30,
             1998 and incorporated herein by reference.

*10.19       Agency Agreement by and between First Security Bank, N.A. and
             GelTex Pharmaceuticals, Inc., dated October 21, 1998. Filed as
             Exhibit 10.1 to GelTex Pharmaceuticals, Inc.'s Quarterly Report on
             Form 10-Q for the quarter ended September 30, 1998 and incorporated
             herein by reference.

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*10.20       Lease Agreement by and between First Security Bank, N.A. and GelTex
             Pharmaceuticals, Inc., dated October 21, 1998. Filed as Exhibit
             10.2 to GelTex Pharmaceuticals, Inc.'s Quarterly Report on Form
             10-Q for the quarter ended September 30, 1998 and incorporated
             herein by reference.

*10.21**     Manufacturing and Supply Agreement (United States) between RenaGel
             LLC and Circa Pharmaceuticals, Inc., dated as of July 31, 1998.
             Filed as Exhibit 10.4 to GelTex Pharmaceuticals, Inc.'s Quarterly
             Report on Form 10-Q for the quarter ended June 30, 1998.

*10.22#      Letter Agreement between GelTex Pharmaceuticals, Inc. and Dr.
             Douglas Reed, dated as of September 4, 1998. Filed as Exhibit 10.1
             to GelTex Pharmaceuticals, Inc.'s Quarterly Report on Form 10-Q for
             the quarter ended March 31, 1999 and incorporated herein by
             reference.

*10.23#      Promissory Note in favor of GelTex Pharmaceuticals, Inc. executed
             by Dr. Douglas Reed, dated December 1, 1998. Filed as Exhibit 10.2
             to GelTex Pharmaceuticals, Inc.'s Quarterly Report on Form 10-Q for
             the quarter ended March 31, 1999 and incorporated herein by
             reference.

*10.24#      Promissory Note in favor of GelTex Pharmaceuticals, Inc. executed
             by Dr. Douglas Reed, dated December 31, 1998. Filed as Exhibit 10.3
             to GelTex Pharmaceuticals, Inc.'s Quarterly Report on Form 10-Q for
             the quarter ended March 31, 1999 and incorporated herein by
             reference.

*10.25#      Promissory Note in favor of GelTex Pharmaceuticals, Inc. executed
             by Dr. Douglas Reed and Linda Reed, dated December 31, 1998. Filed
             as Exhibit 10.4 to GelTex Pharmaceuticals, Inc.'s Quarterly Report
             on Form 10-Q for the quarter ended March 31, 1999 and incorporated
             herein by reference.

*10.26#      Amendment to Promissory Note in favor of GelTex Pharmaceuticals,
             Inc. executed by Dr. Douglas Reed on December 1, 1998. Filed as
             Exhibit 10.1 to GelTex Pharmaceuticals, Inc.'s Quarterly Report on
             Form 10-Q for the quarter ended September 30, 1999.

*10.27#      Amendment to Promissory Note in favor of GelTex Pharmaceuticals,
             Inc. executed by Dr. Douglas Reed on December 31, 1998. Filed as
             Exhibit 10.2 to GelTex Pharmaceuticals, Inc.'s Quarterly Report on
             Form 10-Q for the quarter ended September 30, 1999.

*10.28       Purchase and Sale Agreement between Barry L. Solar and Robert L.
             Solar as Trustees of 211 Second Avenue Realty Trust and GelTex
             Pharmaceuticals, Inc., dated as of July 26, 1999. Filed as Exhibit
             10.4 to GelTex Pharmaceuticals, Inc.'s Quarterly Report on Form
             10-Q for the quarter ended June 30, 1999 and incorporated herein by
             reference.

*10.29       Agreement and Plan of Merger, dated as of August 13, 1999, by and
             among GelTex Pharmaceuticals, Inc., Shine Acquisition Sub, Inc. and
             SunPharm Corporation. Filed as Exhibit 2 to GelTex Pharmaceuticals,
             Inc.'s Registration Statement on Form S-4 (File No. 333-88459) and
             incorporated herein by reference.

*10.30       Common Stock Purchase Agreement dated as of March 7, 2000 by and
             among the Registrant and certain purchasers named therein. Filed as
             Exhibit 10.1 to GelTex Pharmaceuticals, Inc.'s Current Report on
             Form 8-K dated March 6, 2000.

*10.31       Common Stock Purchase Agreement dated as of March 7, 2000 by and
             between the Registrant and Acqua Wellington North American Equities
             Fund, Ltd. Filed as Exhibit 10.2 to GelTex Pharmaceuticals, Inc.'s
             Current Report on Form 8-K dated March 6, 2000.

*10.32**     Supply Agreement dated as of November 9, 1999 by and between
             Salsbury Chemicals, Inc. and GelTex Pharmaceuticals, Inc.

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10.33**      GT 102-279 Collaboration Agreement between the Registrant and
             Sankyo Pharma, Inc. dated as of December 23, 1999, is filed
             herewith.

10.34**      Collaboration Agreement between the Registrant and Sankyo Pharma,
             Inc. dated as of December 23, 1999, is filed herewith.

*21          GelTex Pharmaceuticals, Inc.'s subsidiaries.

*23.1        Consent of Ernst & Young LLP, independent accountants.

*23.2        Consent of PricewaterhouseCoopers LLP, independent accountants.

*24          Power of Attorney.

*27.1        Financial Data Schedule.

*99.1        RenaGel LLC Financial Statements For the Years Ended December 31,
             1999 and 1998 and the Period June 6, 1997 (date of inception)
             through December 31, 1997.

---------------

*   Indicates exhibits previously filed with the Securities and Exchange
    Commission and incorporated herein by reference.

**  Certain confidential material contained in Exhibits 10.2, 10.10, 10.11,
    10.13, 10.14, 10.21, 10.32, 10.33 and 10.34 has been omitted and filed
    separately with the Securities and Exchange Commission.

#   Identifies a management contract or compensatory plan or arrangement in
    which an executive officer or director of GelTex Pharmaceuticals, Inc.
    participants.

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