<PAGE>   1
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                   FORM 10-K/A

 [X]      ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
                            AND EXCHANGE ACT OF 1934
                   For the fiscal year ended DECEMBER 31, 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: 1-13115

                         EQUITY OFFICE PROPERTIES TRUST
             (Exact name of registrant as specified in its charter)

<TABLE>
<S>                                                                  <C>
                       MARYLAND                                                     36-4151656
(State or other jurisdiction of incorporation or organization)        (I.R.S. Employer Identification No.)
                TWO NORTH RIVERSIDE PLAZA,                                            60606
               SUITE 2100, CHICAGO, ILLINOIS                                        (Zip Code)
         (Address of principal executive offices)
</TABLE>

                                 (312) 466-3300
              (Registrant's telephone number, including area code)

           SECURITIES REGISTERED PURSUANT TO SECTION 12(b) OF THE ACT:

<TABLE>
<S>                                                                                   <C>
                        Title of each class                                             Name of each exchange on which registered

               Common Shares of Beneficial Interest,                                             New York Stock Exchange
             $.01 par value per share ("Common Shares")

          8.98% Series A Cumulative Redeemable Preferred                                         New York Stock Exchange
                   Shares of Beneficial Interest,
              liquidation preference $25.00 per share

          5.25% Series B Convertible, Cumulative                                                 New York Stock Exchange
       Redeemable Preferred Shares of Beneficial Interest,
              liquidation preference $50.00 per share

          8.625% Series C Cumulative Redeemable Preferred                                        New York Stock Exchange
                   Shares of Beneficial Interest,
              liquidation preference $25.00 per share
</TABLE>

           SECURITIES REGISTERED PURSUANT TO SECTION 12(g) OF THE ACT:

                                     (None)

      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 (of for such shorter period that the
registrant was required to file such report), and (2) has been subject to such
filing requirements for the past 90 days. [X] Yes [ ] 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 the 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 of the Common Shares held by non-affiliates of
the registrant as of March 1, 2000 was $5,873,438,850.

      On March 1, 2000, 247,941,710 of the registrant's Common Shares were
outstanding.
<PAGE>   2

                       DOCUMENTS INCORPORATED BY REFERENCE

      Portions of the registrant's proxy statement for the annual shareholders'
meeting to be held in 2000 are incorporated by reference into Part III.



                                       2
<PAGE>   3


                                     PART IV

ITEM 14. EXHIBITS, FINANCIAL STATEMENT SCHEDULES, AND REPORTS OF FORM 8-K

         (a)(3)   Exhibits:

                  Item 14(a)(3) is amended to renumber Exhibit 3.6 as Exhibit
                  3.6.1 and add Exhibits 3.6.2 and 3.6.3 and to renumber
                  Exhibit 10.1 as 10.1.1 and add Exhibits 10.1.2 through
                  10.1.6 as set forth below:


            Exhibit No.       Exhibit Description
            -----------       -------------------

                2.1           Agreement and Plan of Merger, dated as of February
                              11, 2000, among the Company, the Operating
                              Partnership, Cornerstone Properties Inc. and
                              Cornerstone Properties Limited Partnership
                              (incorporated herein by reference to Exhibit 2.1
                              to the Company's Current Report on Form 8-K dated
                              February 11, 2000)

                3.1           Articles of Amendment and Restatement of
                              Declaration of Trust of the Company (incorporated
                              herein by reference to Exhibit 4.1 to the
                              Company's Registration Statement on Form S-11
                              (Reg. No. 333-26629))

                3.2*          Articles Supplementary of the Company, dated
                              December 15, 1997 and filed with the Maryland
                              State Department of Assessments and Taxation on
                              December 17, 1997

                3.3*          Articles Supplementary of the Company, dated
                              February 18, 1998 and filed with the Maryland
                              State Department of Assessments and Taxation on
                              February 19, 1998

                3.4           Articles Supplementary of the Company, dated
                              December 1, 1998 as filed with the Maryland State
                              Department of Assessments and Taxation on December
                              4, 1998 (incorporated herein by reference to
                              Exhibit 4.3 of the Company's Registration
                              Statement on Form 8-A dated December 1, 1998)

                3.5**         Articles Supplementary of the Company, dated
                              February 28, 2000 and filed with the Maryland
                              State Department of Assessments and Taxation on
                              March 17, 2000

                3.6.1         Bylaws of the Company (incorporated herein by
                              reference to Exhibit 3.2 of the Company's Current
                              Report on Form 8-K filed with the SEC on
                              September 30, 1998)

                3.6.2+        Amendment Nos. 3 and 4 to the Bylaws of the
                              Company

                3.6.3+        Amended Bylaws of the Company

                4.1*          Indenture, dated as of September 2, 1997, between
                              the Operating Partnership and State Street Bank
                              and Trust Company

                4.2*          First Supplemental Indenture, dated as of February
                              9, 1998, between the Operating Partnership and
                              State Street Bank and Trust Company

                4.3           Form of 6.375% Note due 2003 (incorporated herein
                              by reference to Exhibit 4.4 of the Operating
                              Partnership's Registration Statement on Form S-4
                              (Reg. No. 333-47347))

                4.4           Form of 6.625% Note due 2005 (incorporated herein
                              by reference to Exhibit 4.5 of the Operating
                              Partnership's Registration Statement on Form S-4
                              (Reg. No. 333-47347))

                4.5           Form of 6.750% Note due 2008 (incorporated herein
                              by reference to Exhibit 4.6 of the Operating
                              Partnership's Registration Statement of

                                       3
<PAGE>   4

                              Form S-4 (Reg. No. 333-47347))

                4.6           Form of 7.250% Note due 2018 (incorporated herein
                              by reference to Exhibit 4.7 of the Operating
                              Partnership's Registration Statement on Form S-4
                              (Reg. No. 333-47347))

                4.7           Form of 6.376% Mandatory Par Put Remarketed
                              Securities due 2012 (incorporated herein by
                              reference to Exhibit 4.8 of the Operating
                              Partnership's Registration Statement on Form S-4
                              (Reg. No. 333-47347))

                4.8           $30,000,000 7.24% Senior Note due 2004
                              (incorporated herein by reference to Exhibit 4.9
                              of the Operating Partnership's Registration
                              Statement on Form S-4 (Reg. No. 333-47347))

                4.9           $50,000,000 7.36% Senior Note due 2005
                              (incorporated herein by reference to Exhibit 4.10
                              of the Operating Partnership's Registration
                              Statement on Form S-4 (Reg. No. 333-47347))

                4.10          $50,000,000 7.44% Senior Note due 2006
                              (incorporated herein by reference to Exhibit 4.11
                              to the Operating Partnership's Registration
                              Statement on Form S-4 (Reg. No. 333-47347))

                4.11          $50,000,000 7.41% Senior Note due 2007
                              (incorporated herein by reference to Exhibit 4.12
                              to the Operating Partnership's Registration
                              Statement on Form S-4 (Reg. No. 333-47347))

                4.12          Form of 6.50% Notes due 2004 (incorporated herein
                              by reference to Exhibit 4.3 of the Operating
                              Partnership's Registration Statement on Form S-4
                              (Reg. No. 333-61469))

                4.13          Form of 6.763% Notes due 2007 (incorporated herein
                              by reference to Exhibit 4.4 of the Operating
                              Partnership's Registration Statement on Form S-4
                              (Reg. No. 333-61469))

                4.14          Form of 7.25% Notes due 2028 (incorporated herein
                              by reference to Exhibit 4.5 of the Operating
                              Partnership's Registration Statement on Form S-4
                              (Reg. No. 333-61469))

                4.15          Form of 6.375% Notes due 2002 (incorporated herein
                              by reference to Exhibit 4.1 of the Operating
                              Partnership's Current Report on Form 8-K filed
                              with the SEC on January 25, 1999)

                4.16          Form of 6.5% Notes due 2004 (incorporated herein
                              by reference to Exhibit 4.2 of the Operating
                              Partnership's Current Report on Form 8-K filed
                              with the SEC on January 25, 1999)

                4.17          Form of 6.8% Notes due 2009 (incorporated herein
                              by reference to Exhibit 4.3 of the Operating
                              Partnership's Current Report on Form 8-K filed
                              with the SEC on January 25, 1999)

                4.18          Form of 7.5% Notes due April 19, 2029
                              (incorporated herein by reference to Exhibit 4.23
                              of the Operating Partnership's Current Report on
                              Form 8-K filed with the SEC on April 19, 1999)

                4.19          Form of $400,000,000 8.375% Note due March 15,
                              2006 (incorporated herein by reference to Exhibit
                              4.25 of the Operating

                                       4
<PAGE>   5

                              Partnership's Form 8-K dated March 24, 2000)

                4.20          Form of $100,000,000 8.375% Note due March 15,
                              2006 (incorporated herein by reference to Exhibit
                              4.26 of the Operating Partnership's Form 8-K dated
                              March 24, 2000)

                4.21**        First Amendment to Second Amended and Restated
                              Revolving Credit Agreement

                4.22**        Fixed Rate Promissory Note with The Chase
                              Manhattan Bank

                4.23**        Second Amended and Restated Revolving Credit
                              Facility $1 Billion Revolving Credit Facility
                              dated as of May 29, 1998

                10.1.1*       Agreement of Limited Partnership of the Operating
                              Partnership, dated as of July 3, 1997, as amended

                10.1.2+       Fifth Amendment to Agreement of Limited
                              Partnership of EOP Operating Limited Partnership

                10.1.3+       Amendment to Agreement of Limited Partnership of
                              EOP Operating Limited Partnership

                10.1.4+       Seventh Amendment to Agreement of Limited
                              Partnership of EOP Operating Limited Partnership

                10.1.5+       Eighth Amendment to Agreement of Limited
                              Partnership of EOP Operating Limited Partnership

                10.1.6+       Tenth Amendment to Agreement of Limited
                              Partnership of EOP Operating Limited Partnership

                10.2*         Registration Rights Agreement, dated as of July
                              11, 1997, among the Company and the persons named
                              therein

                10.3*         Noncompetition Agreement between the Company and
                              Samuel Zell

                10.4*         Each member of the Company's Board of Trustees and
                              each Executive Officer of the Company has entered
                              into an Indemnification Agreement with the
                              Company. These Indemnification Agreements are
                              identical in all material respects. The schedule
                              below sets for the terms of each Indemnification
                              Agreement not filed which differ from the copy of
                              the example Indemnification Agreement (between the
                              Company and Samuel Zell, dated as of October 9,
                              1996), which is filed as Exhibit 10.6 to the
                              Company's Annual Report on Form 10-K for the year
                              ended December 31, 1997, as amended:

                              Name                              Date as of
                              ----                              ----------
                              Timothy H. Callahan                10/9/96
                              Richard D. Kincaid                 3/14/97
                              Sheli Z. Rosenberg                 3/12/97
                              Thomas E. Dobrowski                7/11/97
                              James D. Harper, Jr.               7/11/97
                              Jerry M. Reinsdorf                 7/11/97
                              William M. Goodyear                7/11/97


                                       5
<PAGE>   6
                              David K. McKown                    7/11/97
                              H. Jon Runstad                     12/18/97
                              Edwin N. Sidman                    12/24/97
                              D.J. Andre de Bock                 5/15/98
                              Michael A. Steele                  10/9/96
                              Stanley M. Stevens                 10/9/96

                10.5          Stock Option Agreement by and among Cornerstone
                              Properties Inc., the Company, Deutsche Bank AG and
                              Deutscher Herold Lebensversicherungs-AG dated as
                              of February 11, 2000 (incorporated herein by
                              reference to Exhibit 10.1 to the Company's Current
                              Report on Form 8-K dated February 11, 2000)

                10.9**        Equity Office Supplemental Retirement Savings
                              Plan, including the first and second amendment

                12.1**        Statement Regarding Computation of Ratios

                21.1**        List of Subsidiaries

                23.1**        Consent of Independent Auditors

                24.1**        Power of Attorney (included in signature page)

                27.1**        Financial Data Schedule

                99.1**        Equity Office Properties Trust 1997 Non-Qualified
                              Employee Share Purchase Plan Financial Statements
                              as of and for the years ended December 31, 1999
                              and 1998

          *     Incorporated herein by reference to the same-numbered exhibit to
                the Company's Annual Report on Form 10-K for the year ended
                December 31, 1997, as amended

          **    Previously filed

          +     Filed herewith

                                       6
<PAGE>   7

                                   SIGNATURES

            Pursuant to the requirements of Section 13 or 15(d) of the
Securities Exchange Act of 1934, as amended, the Registrant has duly caused this
report to be signed on its behalf by the undersigned, thereunto duly authorized,
in Chicago, Illinois, as of the 11th day of May, 2000.

                                    EQUITY OFFICE PROPERTIES TRUST

                                    By:     /s/ STANLEY M. STEVENS
                                       -----------------------------------
                                       Stanley M. Stevens
                                       Executive Vice President, Chief
                                       Legal Counsel and Secretary


                                       7
<PAGE>   8



                                  EXHIBIT INDEX


             Exhibit No.      Exhibit Description
             ----------       -------------------

                2.1           Agreement and Plan of Merger, dated as of February
                              11, 2000, among the Company, the Operating
                              Partnership, Cornerstone Properties Inc. and
                              Cornerstone Properties Limited Partnership
                              (incorporated herein by reference to Exhibit 2.1
                              to the Company's Current Report on Form 8-K dated
                              February 11, 2000)

                3.1           Articles of Amendment and Restatement of
                              Declaration of Trust of the Company (incorporated
                              herein by reference to Exhibit 4.1 to the
                              Company's Registration Statement on Form S-11
                              (Reg. No. 333-26629))

                3.2*          Articles Supplementary of the Company, dated
                              December 15, 1997 and filed with the Maryland
                              State Department of Assessments and Taxation on
                              December 17, 1997

                3.3*          Articles Supplementary of the Company, dated
                              February 18, 1998 and filed with the Maryland
                              State Department of Assessments and Taxation on
                              February 19, 1998

                3.4           Articles Supplementary of the Company, dated
                              December 1, 1998 as filed with the Maryland State
                              Department of Assessments and Taxation on December
                              4, 1998 (incorporated herein by reference to
                              Exhibit 4.3 of the Company's Registration
                              Statement on Form 8-A dated December 1, 1998)

                3.5**         Articles Supplementary of the Company, dated
                              February 28, 2000 and filed with the Maryland
                              State Department of Assessments and Taxation on
                              March 17, 2000

                3.6.1         Bylaws of the Company (incorporated herein by
                              reference to Exhibit 3.2 of the Company's Current
                              Report on Form 8-K filed with the SEC on
                              September 30, 1998)

                3.6.2+        Amendment Nos. 3 and 4 to the Bylaws of the
                              Company

                3.6.3+        Amended Bylaws of the Company

                4.1*          Indenture, dated as of September 2, 1997, between
                              the Operating Partnership and State Street Bank
                              and Trust Company

                4.2*          First Supplemental Indenture, dated as of February
                              9, 1998, between the Operating Partnership and
                              State Street Bank and Trust Company

                4.3           Form of 6.375% Note due 2003 (incorporated herein
                              by reference to Exhibit 4.4 of the Operating
                              Partnership's Registration Statement on Form S-4
                              (Reg. No. 333-47347))

                4.4           Form of 6.625% Note due 2005 (incorporated herein
                              by reference to Exhibit 4.5 of the Operating
                              Partnership's Registration Statement on Form S-4
                              (Reg. No. 333-47347))

                4.5           Form of 6.750% Note due 2008 (incorporated herein
                              by reference to Exhibit 4.6 of the Operating
                              Partnership's Registration Statement of Form S-4
                              (Reg. No. 333-47347))

                4.6           Form of 7.250% Note due 2018 (incorporated herein
                              by reference to Exhibit 4.7 of the Operating
                              Partnership's Registration Statement on Form S-4
                              (Reg. No. 333-47347))

                4.7           Form of 6.376% Mandatory Par Put Remarketed
                              Securities due 2012

                                       8
<PAGE>   9
                              (incorporated herein by reference to Exhibit 4.8
                              of the Operating Partnership's Registration
                              Statement on Form S-4 (Reg. No. 333-47347))

                4.8           $30,000,000 7.24% Senior Note due 2004
                              (incorporated herein by reference to Exhibit 4.9
                              of the Operating Partnership's Registration
                              Statement on Form S-4 (Reg. No. 333-47347))

                4.9           $50,000,000 7.36% Senior Note due 2005
                              (incorporated herein by reference to Exhibit 4.10
                              of the Operating Partnership's Registration
                              Statement on Form S-4 (Reg. No. 333-47347))

                4.10          $50,000,000 7.44% Senior Note due 2006
                              (incorporated herein by reference to Exhibit 4.11
                              to the Operating Partnership's Registration
                              Statement on Form S-4 (Reg. No. 333-47347))

                4.11          $50,000,000 7.41% Senior Note due 2007
                              (incorporated herein by reference to Exhibit 4.12
                              to the Operating Partnership's Registration
                              Statement on Form S-4 (Reg. No. 333-47347))

                4.12          Form of 6.50% Notes due 2004 (incorporated herein
                              by reference to Exhibit 4.3 of the Operating
                              Partnership's Registration Statement on Form S-4
                              (Reg. No. 333-61469))

                4.13          Form of 6.763% Notes due 2007 (incorporated herein
                              by reference to Exhibit 4.4 of the Operating
                              Partnership's Registration Statement on Form S-4
                              (Reg. No. 333-61469))

                4.14          Form of 7.25% Notes due 2028 (incorporated herein
                              by reference to Exhibit 4.5 of the Operating
                              Partnership's Registration Statement on Form S-4
                              (Reg. No. 333-61469))

                4.15          Form of 6.375% Notes due 2002 (incorporated herein
                              by reference to Exhibit 4.1 of the Operating
                              Partnership's Current Report on Form 8-K filed
                              with the SEC on January 25, 1999)

                4.16          Form of 6.5% Notes due 2004 (incorporated herein
                              by reference to Exhibit 4.2 of the Operating
                              Partnership's Current Report on Form 8-K filed
                              with the SEC on January 25, 1999)

                4.17          Form of 6.8% Notes due 2009 (incorporated herein
                              by reference to Exhibit 4.3 of the Operating
                              Partnership's Current Report on Form 8-K filed
                              with the SEC on January 25, 1999)

                4.18          Form of 7.5% Notes due April 19, 2029
                              (incorporated herein by reference to Exhibit 4.23
                              of the Operating Partnership's Current Report on
                              Form 8-K filed with the SEC on April 19, 1999)

                4.19          Form of $400,000,000 8.375% Note due March 15,
                              2006 (incorporated herein by reference to Exhibit
                              4.25 of the Operating Partnership's Form 8-K dated
                              March 24, 2000)

                4.20          Form of $100,000,000 8.375% Note due March 15,
                              2006 (incorporated herein by reference to Exhibit
                              4.26 of the Operating Partnership's Form 8-K dated
                              March 24, 2000)

                4.21**        First Amendment to Second Amended and Restated
                              Revolving Credit


                                       9
<PAGE>   10

                              Agreement

                4.22**        Fixed Rate Promissory Note with The Chase
                              Manhattan Bank

                4.23**        Second Amended and Restated Revolving Credit
                              Facility $1 Billion Revolving Credit Facility
                              dated as of May 29, 1998

                10.1.1*       Agreement of Limited Partnership of the Operating
                              Partnership, dated as of July 3, 1997, as amended

                10.1.2+       Fifth Amendment to Agreement of Limited
                              Partnership of EOP Operating Limited Partnership

                10.1.3+       Amendment to Agreement of Limited Partnership of
                              EOP Operating Limited Partnership

                10.1.4+       Seventh Amendment to Agreement of Limited
                              Partnership of EOP Operating Limited Partnership

                10.1.5+       Eighth Amendment to Agreement of Limited
                              Partnership of EOP Operating Limited Partnership

                10.1.6+       Tenth Amendment to Agreement of Limited
                              Partnership of EOP Operating Limited Partnership

                10.2*         Registration Rights Agreement, dated as of July
                              11, 1997, among the Company and the persons named
                              therein

                10.3*         Noncompetition Agreement between the Company and
                              Samuel Zell

                10.4*         Each member of the Company's Board of Trustees and
                              each Executive Officer of the Company has entered
                              into an Indemnification Agreement with the
                              Company. These Indemnification Agreements are
                              identical in all material respects. The schedule
                              below sets for the terms of each Indemnification
                              Agreement not filed which differ from the copy of
                              the example Indemnification Agreement (between the
                              Company and Samuel Zell, dated as of October 9,
                              1996), which is filed as Exhibit 10.6 to the
                              Company's Annual Report on Form 10-K for the year
                              ended December 31, 1997, as amended:


                              Name                           Date as of
                              ----                           ----------
                              Timothy H. Callahan             10/9/96
                              Richard D. Kincaid              3/14/97
                              Sheli Z. Rosenberg              3/12/97
                              Thomas E. Dobrowski             7/11/97
                              James D. Harper, Jr.            7/11/97
                              Jerry M. Reinsdorf              7/11/97
                              William M. Goodyear             7/11/97
                              David K. McKown                 7/11/97
                              H. Jon Runstad                  12/18/97
                              Edwin N. Sidman                 12/24/97
                              D.J. Andre de Bock              5/15/98
                              Michael A. Steele               10/9/96
                              Stanley M. Stevens              10/9/96

                10.5          Stock Option Agreement by and among Cornerstone
                              Properties Inc., the

                                       10
<PAGE>   11
                              Company, Deutsche Bank AG and Deutscher Herold
                              Lebensversicherungs-AG dated as of February 11,
                              2000 (incorporated herein by reference to Exhibit
                              10.1 to the Company's Current Report on Form 8-K
                              dated February 11, 2000)

                10.9**        Equity Office Supplemental Retirement Savings
                              Plan, including the first and second amendment

                12.1**        Statement Regarding Computation of Ratios

                21.1**        List of Subsidiaries

                23.1**        Consent of Independent Auditors

                24.1**        Power of Attorney (included in signature page of
                              Form 10-K)

                27.1**        Financial Data Schedule

                99.1**        Equity Office Properties Trust 1997 Non-Qualified
                              Employee Share Purchase Plan Financial Statements
                              as of and for the years ended December 31, 1999
                              and 1998


          *     Incorporated herein by reference to the same-numbered exhibit to
                the Company's Annual Report on Form 10-K for the year ended
                December 31, 1997, as amended

          **    Previously filed

          +     Filed herewith

                                       11