<PAGE>
                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                               AMENDMENT NO. 1 ON
                                   FORM 10-Q/A

                                   (MARK ONE)

[X] QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE
ACT OF 1934 FOR THE PERIOD ENDED SEPTEMBER 30, 2001

[ ] TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE
ACT OF 1934 FOR THE TRANSITION PERIOD FROM _______________________ TO
_________________________.

                           Commission file # 000-28229

                           CALIPER TECHNOLOGIES CORP.
             (Exact name of registrant as specified in its charter)

          Delaware                                      33-0675808
  (State of Incorporation)               (I.R.S. Employer Identification Number)


                               605 FAIRCHILD DRIVE
                          MOUNTAIN VIEW, CA 94043-2234
              (Address and zip code of principal executive offices)

       Registrant's telephone number, including area code: (650) 623-0700



        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 [ ]

COMMON SHARES OUTSTANDING ON NOVEMBER 2, 2001:  24,131,170

                                EXPLANATORY NOTE

        We are filing this amendment to our Quarterly Report on Form 10-Q,
originally filed with the Securities and Exchange Commission on November 14,
2001, solely for the purpose of amending Exhibit 10.33 under Item 6 of Part II.


<PAGE>


ITEM 6. EXHIBITS AND REPORTS ON FORM 8-K

 (a)  Exhibits

<TABLE>
<CAPTION>
   EXHIBIT
   NUMBER                      DESCRIPTION OF DOCUMENT
   ------                      -----------------------
<S>              <C>
   3.1(1)        Amended and Restated Certificate of Incorporation of Caliper.

   3.2(2)        Bylaws of Caliper.

   4.1           Reference is made to Exhibits 3.1 and 3.2.

   4.2(3)        Specimen Stock Certificate.

   10.33(4)      LabChip Solutions Agreement, dated as of September 21, 2001,
                 between Caliper and Amphora Discovery Corp.

   10.34(5)      Consulting Agreement, dated as of October 8, 2001, between
                 Amphora Discovery Corp. and Michael R. Knapp.

   10.35(5)      Founder Restricted Stock Purchase Agreement, dated as of
                 October 8, 2001, between Amphora Discovery Corp. and Michael R.
                 Knapp.

   10.36(5)      Consulting Agreement, dated as of October 14, 2001, between
                 Amphora Discovery Corp. and James L. Knighton.

   10.37(5)      Founder Restricted Stock Purchase Agreement, dated as of
                 October 14, 2001, between Amphora Discovery Corp. and James L.
                 Knighton.

   10.38(4)(5)   Technology Access Agreement Amendment, dated August 20, 2001,
                 between Caliper and Eli Lilly and Company.
</TABLE>


(1)     Previously filed as Exhibit 3.3 to our Registration Statement on Form
        S-1, Registration No. 333-88827.

(2)     Previously filed as Exhibit 3.4 to our Registration Statement on Form
        S-1, Registration No. 333-88827.

(3)     Previously filed as the like-numbered Exhibit to our Registration
        Statement on Form S-1, Registration No. 333-88827.

(4)     Confidential treatment has been requested for a portion of this exhibit.

(5)     Previously filed as the like-numbered Exhibit to our Quarterly Report on
        Form 10-Q which this Form 10-Q/A amends.

(b)     Reports on Form 8-K

        We did not file a Current Report on Form 8-K during the quarter ended
September 30, 2001.


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<PAGE>


                                   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.

                                        CALIPER TECHNOLOGIES CORP.

        March 14, 2002                  By:/s/ DANIEL L. KISNER
                                           --------------------------------
                                             Daniel L. Kisner, M.D.
                                             President and Chief
                                             Executive Officer


                                        By:/s/ ANTHONY T. HENDRICKSON
                                           --------------------------------
                                             Anthony T. Hendrickson
                                             Corporate Controller and Principal
                                             Accounting Officer


                                       2
<PAGE>


<TABLE>
<CAPTION>
EXHIBIT INDEX
<S>                 <C>
      3.1(1)        Amended and Restated Certificate of Incorporation of
                    Caliper.

      3.2(2)        Bylaws of Caliper.

      4.1           Reference is made to Exhibits 3.1 and 3.2.

      4.2(3)        Specimen Stock Certificate.

      10.33(4)      LabChip Solutions Agreement, dated as of September 21, 2001,
                    between Caliper and Amphora Discovery Corp.

      10.34(5)      Consulting Agreement, dated as of October 8, 2001, between
                    Amphora Discovery Corp. and Michael R. Knapp.

      10.35(5)      Founder Restricted Stock Purchase Agreement, dated as of
                    October 8, 2001, between Amphora Discovery Corp. and Michael
                    R. Knapp.

      10.36(5)      Consulting Agreement, dated as of October 14, 2001, between
                    Amphora Discovery Corp. and James L. Knighton.

      10.37(5)      Founder Restricted Stock Purchase Agreement, dated as of
                    October 14, 2001, between Amphora Discovery Corp. and James
                    L. Knighton.

      10.38(4)(5)   Technology Access Agreement Amendment, dated August 20,
                    2001, between Caliper and Eli Lilly and Company.
</TABLE>


(1)     Previously filed as Exhibit 3.3 to our Registration Statement on Form
        S-1, Registration No. 333-88827.

(2)     Previously filed as Exhibit 3.4 to our Registration Statement on Form
        S-1, Registration No. 333-88827.

(3)     Previously filed as the like-numbered Exhibit to our Registration
        Statement on Form S-1, Registration No. 333-88827.

(4)     Confidential treatment has been requested for a portion of this exhibit.

(5)     Previously filed as the like-numbered Exhibit to our Quarterly Report on
        Form 10-Q which this Form 10-Q/A amends.


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