<PAGE>

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

                                 UNITED STATES
                      SECURITIES AND EXCHANGE COMMISSION
                             Washington, DC  20549

                                  ___________
                                  FORM 10-K/A
                               (Amendment No. 3)
                                  ___________

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

                  For the fiscal year ended December 31, 2000

                                       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 0-11749

                                  ___________

                                   SCIOS INC.

             (Exact name of registrant as specified in its charter)

                                  ___________

                  DELAWARE                                  95-3701481
       (State or other jurisdiction of                   (I.R.S. Employer
        incorporation or organization)                  Identification No.)


              820 West Maude Avenue, Sunnyvale, California 94086
                   (Address of principal executive offices)

      Registrant's telephone number, including area code: (408) 616-8200

Securities registered pursuant to Section 12(b) of the Act: NONE

Securities registered pursuant to Section 12(g) of the Act:

                        Common Stock, $0.001 par value
                           Contingent Payment Rights

     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 approximate aggregate market value of voting stock held by
nonaffiliates of the registrant as of March 16, 2001 was $737,569,844.

     As of March 16, 2001, 39,314,425 shares of the registrant's Common Stock
were outstanding.

                      DOCUMENTS INCORPORATED BY REFERENCE
Documents                                                        Form 10-K Part
---------                                                        --------------

Definitive Proxy Statement with respect to the 2001 Annual Meeting of
Stockholders................................................................ III

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

                                EXPLANATORY NOTE

  This amendment to our Annual Report on Form 10-K for the year-ended December
31, 2000 amends "Item 14. Exhibit Index" to add "Exhibit Number 10.42--
Promissory Note dated December 27, 1999 by the Registrant to Chiron
Corporation."  This information was inadvertently omitted from our Form 10-K/A
(Amendment No. 2) filed with the Securities and Exchange Commission on June 20,
2001.  Other than the above-referenced change, the information set forth below
is substantively identical to the information set forth under "Item 14. Exhibit
Index" as set forth in our Annual Report on Form 10-K/A (Amendment No. 2) filed
with the SEC on June 20, 2001.

PART IV

Item 14.  EXHIBITS, FINANCIAL STATEMENT SCHEDULES AND REPORTS ON FORM 8-K

     (a)  (1)  Consolidated Financial Statements. See Index to Consolidated
               Financial Statements at page F-1 of this Form 10-K.

          (2)  Financial Statement Schedules. Omitted because they are not
               required, are not applicable, or the information is included in
               the consolidated financial statements or notes thereto.

          (3)  Exhibits. See Exhibit Index below.

     (b)  Reports on Form 8-K.  None.

                                  EXHIBIT INDEX

<TABLE>
<CAPTION>

  Exhibit
  Number                                                                                                  Reference
------------                                                                                              -----------
<S>          <C>                                                                                          <C>
    3.1      Certificate of Incorporation..............................................................       Q
    3.2      Bylaws....................................................................................       J
   10.1      Biotechnology Research Partners, Ltd. Agreement of Limited Partnership dated
             October 29, 1982; Development Contract, Technology License Agreement and Joint Venture
             Agreement between Biotechnology Research Partners, Ltd. and the Registrant dated December
             29, 1982; and Promissory Note dated December 29, 1982.
                                                                                                              A
   10.2*     1983 Incentive Stock Option Plan, as amended, and form of Stock Option Agreement, Promissory
             Note and Pledge Agreement.................................................................       E
   10.3      Common Stock Purchase Agreement dated April 15, 1985 between the Registrant and American
             Home Products Corporation.................................................................       B
   10.5*     1986 Supplemental Stock Option Plan, as amended, and form of Stock Option Agreement,
             Promissory Note and Pledge Agreement......................................................       E
   10.6      Rights Exercise Agreement between the Registrant and American Home Products Corporation
             dated February 28, 1986 and Letters of March 26, 1986 and May 16, 1986....................       B
   10.11*    1992 Equity Incentive Plan................................................................       H
   10.18     Form of Purchase Option Agreement between each of the limited partners of Nova Technology
             Limited Partnership and Nova..............................................................       I
   10.19*    Nonemployee Director Stock Option Plan....................................................       G
   10.29     CNS Psychiatric Products Agreement dated June 30, 1990 between SmithKline Beecham
             Corporation and Nova......................................................................       N
   10.33     Preferred Stock Purchase Agreement dated December 30, 1994 between the Registrant and
             Genentech, Inc............................................................................       Q
   10.34     Note Agreement dated December 30, 1994 between the Registrant and Genentech, Inc. (See
             Exhibit Number 10.41 below amending the Note Agreement)...................................       Q
   10.35     Assignment of Lease dated March 22, 1995 for premises located at 820 West Maude Avenue,
             Sunnyvale, California (Including as an Exhibit, the Lease for such premises dated January 22,
             1993) (See Exhibit 10.45 below)...........................................................       R
   10.38*    Employment Letter dated September 8, 1998 between the Registrant and
             Richard B. Brewer.........................................................................       T
   10.39     Purchase and Sale Agreement and Joint Escrow Instructions (Mountain View Real Estate Sale)
             dated May 24, 1999 between Alexandria Real Estate Equities, Inc. and Registrant's wholly
             owned Subsidiary Bio-Shore Holdings, Ltd.  Portions of the exhibit have been omitted
             pursuant to a request for confidential treatment..........................................       U
   10.41     First Amendment to Note Agreement and Preferred Stock Purchase Agreement dated November
             3, 1999 between the Registrant and Genentech, Inc. (See Exhibit 10.34 above)..............       V
   10.42     Promissory Note dated December 27, 1999 by the Registrant to Chiron Corporation...........       V
</TABLE>

                                       2
<PAGE>

<TABLE>
<CAPTION>

<S>          <C>                                                                                              <C>
   10.43*    Change of Control Severance Plans with Employees, Officers and Chief Executive Officer....       W
   10.44     Alliance Agreement dated January 10, 2001 between the Registrant, Innovex L.P. and PharmaBio
             Development Inc. (including a Warrant Agreement between the Registrant and PharmaBio
             Development Inc. attached thereto as Exhibit B).  Portions of the exhibit have been omitted
             pursuant to a request for confidential treatment..........................................       Y
   10.45     Amendment No. 4 to Lease dated January 22, 1993 for premises located at 820 West Maude
             Avenue, Sunnyvale, California (See Exhibit 10.35 above)...................................       Z
   10.46     Lease Agreement dated November 17, 1995 for premises located at 820 West Maude Avenue,
             Sunnyvale, California.....................................................................       Z
   10.47     Sublease Agreement dated March 24, 1999 for premises located at 749 North Mary Avenue,
             Sunnyvale, California.....................................................................       Z
   21.2      Subsidiaries of the Registrant............................................................       V
   23.1**    Consent of PricewaterhouseCoopers LLP.....................................................
   24.1**    Powers of Attorney. ......................................................................
----------------------
</TABLE>
     *       Management contract or compensatory plan or arrangement.

    **       Previously filed.

     A       Filed as an exhibit to Form S-1 Registration Statement
             (File No. 2-86086), as amended, and incorporated herein by
             reference.

     B       Filed as an exhibit to Form S-1 Registration Statement
             (File No. 33-3186), as amended, and incorporated herein by
             reference.

     E       Filed as an exhibit to Annual Report on Form 10-K for fiscal year
             1988 and incorporated herein by reference.

     G       Filed as an exhibit to Form S-8 Registration Statement (File No.
             33-39878) filed on April 8, 1991 and incorporated herein by
             reference.

     H       Filed as an exhibit to Annual Report on Form 10-K for fiscal year
             1991 and incorporated herein by reference.

     I       Filed as an exhibit to Form S-1 Registration Statement (File No.
             33-14937) filed on behalf of Nova Technology Limited Partnership
             and incorporated herein by reference.

     J       Filed as an exhibit to Form S-4 Registration Statement (File No.
             33-49846) filed on July 22, 1992 and incorporated herein by
             reference.

     N       Filed as an exhibit to Nova's Annual Report on Form 10-K for
             fiscal year 1990 and incorporated herein by reference

     Q       Filed as an exhibit to Annual Report on Form 10-K for fiscal year
             1994 and incorporated herein by reference.

     R       Filed as an exhibit to Quarterly Report on Form 10-Q for quarter
             ended March 31, 1995 and incorporated herein by reference.

     T       Filed as an exhibit to Annual Report on Form 10-K for fiscal year
             1998 and incorporated herein by reference.

     U       Filed as an exhibit to Quarterly Report on Form 10-Q for the
             quarter ended September 30, 1999 and incorporated herein by
             reference.

     V       Filed as an exhibit to Annual Report on Form 10-K for fiscal year
             1999 and incorporated herein by reference.

     W       Filed as exhibits to Report on Form 8-K dated January 24, 2000 and
             incorporated herein by reference.

     Y       Filed as an exhibit to Annual Report on Form 10-K for fiscal year
             2000 and incorporated herein by reference.

     Z       Filed as an exhibit to Annual Report on Form 10-K/A (Amendment
             No. 2) for fiscal year 2000 and incorporated herein by reference.


                                       3
<PAGE>

                                   SIGNATURES

         Pursuant to the requirements of Section 13 or 15(d)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.

                                   SCIOS INC.

Date:  June 21, 2001               By:  /s/ Richard B. Brewer
                                        --------------------------------------
                                        Richard B. Brewer
                                        President and Chief Executive Officer


                                       4