<PAGE>   1
   As filed with the Securities and Exchange Commission on September 20, 2001
                                                    Registration No. 333-
================================================================================

                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

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

                                    FORM S-8
                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933

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

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

        DELAWARE                                        33-0675808
(State of Incorporation)                    (I.R.S. Employer Identification No.)

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

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

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

                           1999 EQUITY INCENTIVE PLAN
                        1999 EMPLOYEE STOCK PURCHASE PLAN
                 1999 NON-EMPLOYEE DIRECTORS' STOCK OPTION PLAN
                            (Full title of the plans)


                                JAMES L. KNIGHTON
                             CHIEF FINANCIAL OFFICER
                           CALIPER TECHNOLOGIES CORP.
                               605 FAIRCHILD DRIVE
                          MOUNTAIN VIEW, CA 94043-2234
                                 (650) 623-0700
            (Name, address, including zip code, and telephone number,
                   including area code, of agent for service)

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

                                   COPIES TO:
                              ROBERT L. JONES, ESQ.
                              BRETT D. WHITE, ESQ.
                               COOLEY GODWARD LLP
                              FIVE PALO ALTO SQUARE
                               3000 EL CAMINO REAL
                           PALO ALTO, CALIFORNIA 94306
                                 (650) 843-5000

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


<PAGE>   2

                         CALCULATION OF REGISTRATION FEE

<TABLE>
<CAPTION>
===============================================================================================================================
                                                        PROPOSED MAXIMUM         PROPOSED MAXIMUM
   TITLE OF SECURITIES      AMOUNT TO BE REGISTERED         OFFERING                 AGGREGATE                AMOUNT OF
     TO BE REGISTERED                 (1)              PRICE PER SHARE (2)      OFFERING PRICE (2)        REGISTRATION FEE
--------------------------- ------------------------ ------------------------ ------------------------ ------------------------
<S>                                <C>                                            <C>                         <C>
 Common Stock (par                                   (see Notes to Calculation
   value $0.001)                   1,555,436           of Registration Fee)        $16,798,173.38              $4,199.54
===============================================================================================================================
</TABLE>

(1)      1,350,058 shares to be registered pursuant to the 1999 Equity Incentive
         Plan, 128,361 shares to be registered pursuant to the 1999 Employee
         Stock Purchase Plan and 77,017 shares to be registered pursuant to the
         1999 Non-Employee Directors' Stock Option Plan. This Registration
         Statement shall cover any additional shares of Common Stock which
         become issuable under the plans set forth herein by reason of any stock
         dividend, stock split, recapitalization or any other similar
         transaction without receipt of consideration which results in an
         increase in the number of shares of the Registrant's outstanding Common
         Stock.

(2)      Estimated solely for the purpose of calculating the amount of the
         registration fee pursuant to Rule 457(h). The price per share and
         aggregate offering price of the shares to be offered under the these
         plans are based upon (a) the weighted average exercise price for shares
         issuable pursuant to outstanding options granted under the 1999 Equity
         Incentive Plan and (b) the average of the high and low prices of the
         Registrant's Common Stock on September 18, 2001 as reported on the
         Nasdaq National Market (pursuant to Rule 457(c) under the Act) for
         shares reserved for future issuance under (i) the 1999 Equity Incentive
         Plan, (ii) the 1999 Employee Stock Purchase Plan and (iii) the 1999
         Non-Employee Directors' Stock Option Plan. The registration fee is
         calculated as follows:


<TABLE>
<CAPTION>
                          PLAN                      NUMBER OF SHARES      OFFERING PRICE PER SHARE    AGGREGATE OFFERING
                                                                                                             PRICE
         --------------------------------------- ------------------------ ------------------------- ------------------------
<S>                                                      <C>                       <C>                    <C>
         Shares issuable pursuant to                     27,718                    $15.19                 $421,036.42
         outstanding options under the 1999
         Equity Incentive Plan

         Shares reserved for future issuance            1,322,340                  $10.72                $14,175,484.80
         under the 1999 Equity Incentive Plan

         Shares reserved for future issuance             128,361                   $10.72                $1,376,029.92
         under the 1999 Employee Stock
         Purchase Plan

         Shares reserved for future issuance             77,017                    $10.72                 $825,622.24
         under the 1999 Non-Employee
         Directors' Stock Option Plan
                                                 ------------------------ ------------------------- ------------------------
                         TOTAL                          1,555,436                                       $16,798,173.38
</TABLE>


<PAGE>   3


                    INCORPORATION BY REFERENCE OF CONTENTS OF
                      REGISTRATION STATEMENTS ON FORMS S-8

         The contents of Registration Statement on Form S-8 (No. 333-95007)
filed with the Securities and Exchange Commission on January 20, 2000 are
incorporated by reference herein.

         The contents of Registration Statement on Form S-8 (No. 333-40466)
filed with the Securities and Exchange Commission on June 29, 2000 are
incorporated by reference herein.

                                    EXHIBITS

<TABLE>
<CAPTION>
     EXHIBIT
     NUMBER                             DESCRIPTION
<S>             <C>

      4.1(1)     Amended and Restated Certificate of Incorporation of the Registrant.
      4.2(2)     Amended and Restated Bylaws of the Registrant.
      4.3(3)     Specimen Stock Certificate.
      5.1        Opinion of Cooley Godward LLP.
     23.1        Consent of Ernst & Young LLP, independent auditors.
     23.2        Consent of Cooley Godward LLP.  Reference is made to Exhibit 5.1.
     24.1        Power of Attorney.  Reference is made to Signature Page.
     99.2(4)     1999 Equity Incentive Plan.
     99.3(4)     1999 Employee Stock Purchase Plan.
     99.4(4)     1999 Non-Employee Directors' Stock Option Plan.
</TABLE>


(1)  Previously filed as Exhibit 3.3 to the Registration Statement on Form S-1
     (No. 333-88827), as amended, and incorporated herein by reference.

(2)  Previously filed as Exhibit 3.4 to the Registration Statement on Form S-1
     (No. 333-88827), as amended, and incorporated herein by reference.

(3)  Previously filed as Exhibit 4.2 to the Registration Statement on Form S-1
     (No. 333-88827), as amended, and incorporated herein by reference.

(4)  Previously filed as the like-numbered Exhibit to the Registration Statement
     on Form S-8 (No. 333-95007), and incorporated herein by reference.



<PAGE>   4


                                   SIGNATURES

         Pursuant to the requirements of the Securities Act of 1933, as amended,
the Registrant certifies that it has reasonable grounds to believe that it meets
all of the requirements for filing on Form S-8 and has duly caused this
Registration Statement to be signed on its behalf by the undersigned, thereunto
duly authorized, in the City of Mountain View, State of California, September
18, 2001.

                                      Caliper Technologies Corp.

                                      By: /s/ James L. Knighton
                                         -----------------------------------
                                         James L. Knighton
                                         Chief Financial Officer

                                POWER OF ATTORNEY

         KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature
appears below constitutes and appoints Daniel L. Kisner, M.D. and James L.
Knighton, and each or any one of them, his true and lawful attorney-in-fact and
agent, with full power of substitution and resubstitution, for him and in his
name, place and stead, in any and all capacities, to sign any and all amendments
(including post-effective amendments) to this Registration Statement, and to
file the same, with all exhibits thereto, and other documents in connection
therewith, with the Securities and Exchange Commission, granting unto said
attorneys-in-fact and agents, and each of them, full power and authority to do
and perform each and every act and thing requisite and necessary to be done in
connection therewith, as fully to all intents and purposes as he might or could
do in person, hereby ratifying and confirming all that said attorneys-in-fact
and agents, or any of them, or their or his substitutes or substitute, may
lawfully do or cause to be done by virtue hereof.


<PAGE>   5


         Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed by the following persons in the
capacities and on the dates indicated.

<TABLE>
<CAPTION>
              SIGNATURE                                     TITLE                                    DATE
<S>                                         <C>                                               <C>

/s/ Daniel L. Kisner, M.D.                  President, Chief Executive Officer and            September 18, 2001
-----------------------------------         Director (Principal Executive Officer)
     Daniel L. Kisner, M.D.

/s/ James L. Knighton                              Chief Financial Officer                    September 18, 2001
-----------------------------------              (Principal Financial Officer)
     James L. Knighton

/s/ Anthony Hendrickson                              Corporate Controller                     September 18, 2001
-----------------------------------             (Principal Accounting Officer)
     Anthony Hendrickson

/s/ David V. Milligan, Ph.D.                               Director                           September 18, 2001
-----------------------------------
     David V. Milligan, Ph.D.

/s/ Anthony B. Evnin, Ph.D.                                Director                           September 18, 2001
-----------------------------------
     Anthony B. Evnin, Ph.D.

/s/ Regis P. McKenna                                       Director                           September 18, 2001
-----------------------------------
     Regis P. McKenna

/s/ Robert T. Nelsen                                       Director                           September 18, 2001
-----------------------------------
     Robert T. Nelsen
</TABLE>


<PAGE>   6


EXHIBIT INDEX

<TABLE>
<CAPTION>
   EXHIBIT
    NUMBER                                 DESCRIPTION
<S>             <C>
      4.1(1)     Amended and Restated Certificate of Incorporation of the Registrant.
      4.2(2)     Amended and Restated Bylaws of the Registrant.
      4.3(3)     Specimen Stock Certificate.
      5.1        Opinion of Cooley Godward LLP.
     23.1        Consent of Ernst & Young LLP, independent auditors.
     23.2        Consent of Cooley Godward LLP.  Reference is made to Exhibit 5.1.
     24.1        Power of Attorney.  Reference is made to Signature Page.
     99.2(4)     1999 Equity Incentive Plan.
     99.3(4)     1999 Employee Stock Purchase Plan.
     99.4(4)     1999 Non-Employee Directors' Stock Option Plan.
</TABLE>


(1)  Previously filed as Exhibit 3.3 to the Registration Statement on Form S-1
     (No. 333-88827), as amended, and incorporated herein by reference.

(2)  Previously filed as Exhibit 3.4 to the Registration Statement on Form S-1
     (No. 333-88827), as amended, and incorporated herein by reference.

(3)  Previously filed as Exhibit 4.2 to the Registration Statement on Form S-1
     (No. 333-88827), as amended, and incorporated herein by reference.

(4)  Previously filed as the like-numbered Exhibit to the Registration Statement
     on Form S-8 (No. 333-95007), and incorporated herein by reference.
[{"type": "S-8", "sequence": "1", "filename": "f75858s-8.txt", "description": "FORM S-8", "secsgml_size_bytes": 13602}]
{"company-data": {"conformed-name": "CALIPER TECHNOLOGIES CORP", "cik": "0001014672", "assigned-sic": "3826", "irs-number": "330675808", "state-of-incorporation": "DE", "fiscal-year-end": "1231"}, "filing-values": {"form-type": "S-8", "act": "33", "file-number": "333-69722", "film-number": "1741388"}, "business-address": {"street1": "605 FAIRCHILD DR", "street2": "STE 405", "city": "MOUNTAIN VIEW", "state": "CA", "zip": "94043", "phone": "6506230700"}, "mail-address": {"street1": "605 FAIRCHILD DRIVE", "city": "MOUNTAIN VIEW", "state": "CA", "zip": "94043"}}
1
   As filed with the Securities and Exchange Commission on September 20, 2001
                                                    Registration No. 333-
================================================================================

                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

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

                                    FORM S-8
                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933

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

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

        DELAWARE                                        33-0675808
(State of Incorporation)                    (I.R.S. Employer Identification No.)

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

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

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

                           1999 EQUITY INCENTIVE PLAN
                        1999 EMPLOYEE STOCK PURCHASE PLAN
                 1999 NON-EMPLOYEE DIRECTORS' STOCK OPTION PLAN
                            (Full title of the plans)

                                JAMES L. KNIGHTON
                             CHIEF FINANCIAL OFFICER
                           CALIPER TECHNOLOGIES CORP.
                               605 FAIRCHILD DRIVE
                          MOUNTAIN VIEW, CA 94043-2234
                                 (650) 623-0700
            (Name, address, including zip code, and telephone number,
                   including area code, of agent for service)

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

                                   COPIES TO:
                              ROBERT L. JONES, ESQ.
                              BRETT D. WHITE, ESQ.
                               COOLEY GODWARD LLP
                              FIVE PALO ALTO SQUARE
                               3000 EL CAMINO REAL
                           PALO ALTO, CALIFORNIA 94306
                                 (650) 843-5000

                              --------------------
2

                         CALCULATION OF REGISTRATION FEE
===============================================================================================================================
                                                        PROPOSED MAXIMUM         PROPOSED MAXIMUM
   TITLE OF SECURITIES      AMOUNT TO BE REGISTERED         OFFERING                 AGGREGATE                AMOUNT OF
     TO BE REGISTERED                 (1)              PRICE PER SHARE (2)      OFFERING PRICE (2)        REGISTRATION FEE
--------------------------- ------------------------ ------------------------ ------------------------ ------------------------
Common Stock (par                                   (see Notes to Calculation
   value $0.001)                   1,555,436           of Registration Fee)        $16,798,173.38              $4,199.54
===============================================================================================================================
(1)      1,350,058 shares to be registered pursuant to the 1999 Equity Incentive
         Plan, 128,361 shares to be registered pursuant to the 1999 Employee
         Stock Purchase Plan and 77,017 shares to be registered pursuant to the
         1999 Non-Employee Directors' Stock Option Plan. This Registration
         Statement shall cover any additional shares of Common Stock which
         become issuable under the plans set forth herein by reason of any stock
         dividend, stock split, recapitalization or any other similar
         transaction without receipt of consideration which results in an
         increase in the number of shares of the Registrant's outstanding Common
         Stock.

(2)      Estimated solely for the purpose of calculating the amount of the
         registration fee pursuant to Rule 457(h). The price per share and
         aggregate offering price of the shares to be offered under the these
         plans are based upon (a) the weighted average exercise price for shares
         issuable pursuant to outstanding options granted under the 1999 Equity
         Incentive Plan and (b) the average of the high and low prices of the
         Registrant's Common Stock on September 18, 2001 as reported on the
         Nasdaq National Market (pursuant to Rule 457(c) under the Act) for
         shares reserved for future issuance under (i) the 1999 Equity Incentive
         Plan, (ii) the 1999 Employee Stock Purchase Plan and (iii) the 1999
         Non-Employee Directors' Stock Option Plan. The registration fee is
         calculated as follows:
PLAN                      NUMBER OF SHARES      OFFERING PRICE PER SHARE    AGGREGATE OFFERING
                                                                                                             PRICE
         --------------------------------------- ------------------------ ------------------------- ------------------------
Shares issuable pursuant to                     27,718                    $15.19                 $421,036.42
         outstanding options under the 1999
         Equity Incentive Plan

         Shares reserved for future issuance            1,322,340                  $10.72                $14,175,484.80
         under the 1999 Equity Incentive Plan

         Shares reserved for future issuance             128,361                   $10.72                $1,376,029.92
         under the 1999 Employee Stock
         Purchase Plan

         Shares reserved for future issuance             77,017                    $10.72                 $825,622.24
         under the 1999 Non-Employee
         Directors' Stock Option Plan
                                                 ------------------------ ------------------------- ------------------------
                         TOTAL                          1,555,436                                       $16,798,173.38
3

                    INCORPORATION BY REFERENCE OF CONTENTS OF
                      REGISTRATION STATEMENTS ON FORMS S-8

         The contents of Registration Statement on Form S-8 (No. 333-95007)
filed with the Securities and Exchange Commission on January 20, 2000 are
incorporated by reference herein.

         The contents of Registration Statement on Form S-8 (No. 333-40466)
filed with the Securities and Exchange Commission on June 29, 2000 are
incorporated by reference herein.

                                    EXHIBITS
EXHIBIT
     NUMBER                             DESCRIPTION
4.1(1)     Amended and Restated Certificate of Incorporation of the Registrant.
      4.2(2)     Amended and Restated Bylaws of the Registrant.
      4.3(3)     Specimen Stock Certificate.
      5.1        Opinion of Cooley Godward LLP.
     23.1        Consent of Ernst & Young LLP, independent auditors.
     23.2        Consent of Cooley Godward LLP.  Reference is made to Exhibit 5.1.
     24.1        Power of Attorney.  Reference is made to Signature Page.
     99.2(4)     1999 Equity Incentive Plan.
     99.3(4)     1999 Employee Stock Purchase Plan.
     99.4(4)     1999 Non-Employee Directors' Stock Option Plan.
(1)  Previously filed as Exhibit 3.3 to the Registration Statement on Form S-1
     (No. 333-88827), as amended, and incorporated herein by reference.

(2)  Previously filed as Exhibit 3.4 to the Registration Statement on Form S-1
     (No. 333-88827), as amended, and incorporated herein by reference.

(3)  Previously filed as Exhibit 4.2 to the Registration Statement on Form S-1
     (No. 333-88827), as amended, and incorporated herein by reference.

(4)  Previously filed as the like-numbered Exhibit to the Registration Statement
     on Form S-8 (No. 333-95007), and incorporated herein by reference.
4

                                   SIGNATURES

         Pursuant to the requirements of the Securities Act of 1933, as amended,
the Registrant certifies that it has reasonable grounds to believe that it meets
all of the requirements for filing on Form S-8 and has duly caused this
Registration Statement to be signed on its behalf by the undersigned, thereunto
duly authorized, in the City of Mountain View, State of California, September
18, 2001.

                                      Caliper Technologies Corp.

                                      By: /s/ James L. Knighton
                                         -----------------------------------
                                         James L. Knighton
                                         Chief Financial Officer

                                POWER OF ATTORNEY

         KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature
appears below constitutes and appoints Daniel L. Kisner, M.D. and James L.
Knighton, and each or any one of them, his true and lawful attorney-in-fact and
agent, with full power of substitution and resubstitution, for him and in his
name, place and stead, in any and all capacities, to sign any and all amendments
(including post-effective amendments) to this Registration Statement, and to
file the same, with all exhibits thereto, and other documents in connection
therewith, with the Securities and Exchange Commission, granting unto said
attorneys-in-fact and agents, and each of them, full power and authority to do
and perform each and every act and thing requisite and necessary to be done in
connection therewith, as fully to all intents and purposes as he might or could
do in person, hereby ratifying and confirming all that said attorneys-in-fact
and agents, or any of them, or their or his substitutes or substitute, may
lawfully do or cause to be done by virtue hereof.
5

         Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed by the following persons in the
capacities and on the dates indicated.
SIGNATURE                                     TITLE                                    DATE
/s/ Daniel L. Kisner, M.D.                  President, Chief Executive Officer and            September 18, 2001
-----------------------------------         Director (Principal Executive Officer)
     Daniel L. Kisner, M.D.

/s/ James L. Knighton                              Chief Financial Officer                    September 18, 2001
-----------------------------------              (Principal Financial Officer)
     James L. Knighton

/s/ Anthony Hendrickson                              Corporate Controller                     September 18, 2001
-----------------------------------             (Principal Accounting Officer)
     Anthony Hendrickson

/s/ David V. Milligan, Ph.D.                               Director                           September 18, 2001
-----------------------------------
     David V. Milligan, Ph.D.

/s/ Anthony B. Evnin, Ph.D.                                Director                           September 18, 2001
-----------------------------------
     Anthony B. Evnin, Ph.D.

/s/ Regis P. McKenna                                       Director                           September 18, 2001
-----------------------------------
     Regis P. McKenna

/s/ Robert T. Nelsen                                       Director                           September 18, 2001
-----------------------------------
     Robert T. Nelsen
6

EXHIBIT INDEX
EXHIBIT
    NUMBER                                 DESCRIPTION
4.1(1)     Amended and Restated Certificate of Incorporation of the Registrant.
      4.2(2)     Amended and Restated Bylaws of the Registrant.
      4.3(3)     Specimen Stock Certificate.
      5.1        Opinion of Cooley Godward LLP.
     23.1        Consent of Ernst & Young LLP, independent auditors.
     23.2        Consent of Cooley Godward LLP.  Reference is made to Exhibit 5.1.
     24.1        Power of Attorney.  Reference is made to Signature Page.
     99.2(4)     1999 Equity Incentive Plan.
     99.3(4)     1999 Employee Stock Purchase Plan.
     99.4(4)     1999 Non-Employee Directors' Stock Option Plan.
(1)  Previously filed as Exhibit 3.3 to the Registration Statement on Form S-1
     (No. 333-88827), as amended, and incorporated herein by reference.

(2)  Previously filed as Exhibit 3.4 to the Registration Statement on Form S-1
     (No. 333-88827), as amended, and incorporated herein by reference.

(3)  Previously filed as Exhibit 4.2 to the Registration Statement on Form S-1
     (No. 333-88827), as amended, and incorporated herein by reference.

(4)  Previously filed as the like-numbered Exhibit to the Registration Statement
     on Form S-8 (No. 333-95007), and incorporated herein by reference.