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UNITED STATES SECURITIES AND EXCHANGE COMMISSION
 Washington, D.C. 20549
 
 FORM 10-K/A
 (Mark One)
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    ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 For the Fiscal Year Ended December 31, 2005
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    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 0-27892
 SIPEX CORPORATION
 (Exact name of registrant as specified in its charter)
 Delaware
    
    04-6135748(State of Incorporation)
    
    (IRS employer identification number)233 South Hillview Drive, Milpitas, California
    
    95035(Address of principal executive offices)
    
    (Zip Code)
 Registrants telephone number, including area code: (408) 934-7500
Securities registered pursuant to Section 12(b) of the Act: None
Securities registered pursuant to Section 12(g) of the Act:
Common Stock, par value $0.01 per share
Name of exchange on which registered: None
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EXPLANATORY NOTE




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TABLE OF CONTENTS
 PagePart IVItem 15. Exhibits, Financial Statement Schedules and Reports on Form 10-K
    
    
    1Signature
    
    
    2EXHIBIT 23.1EXHIBIT 31.1EXHIBIT 31.2EXHIBIT 32.1EXHIBIT 32.2




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PART IV
 
 Item 15. Exhibits, Financial Statement Schedules and Reports on Form 10-K:
  1.
    
    Consolidated financial statements. The following
consolidated financial statements of the Company and Report of
Independent Registered Public Accounting Firm are incorporated
in Item 8 of this report.
 
 2.
    
    Consolidated Financial Statement Schedules. Consolidated financial statements schedules have been omitted because they are either not
required or are included in the consolidated financial statements or the notes thereto.
 3.
    
    Exhibit: The exhibits listed in the accompanying index to exhibits are filed or
incorporated by reference as part of this Form 10-K.
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SIGNATURES
  SIPEX CORPORATIONBy:
    /s/ RALPH SCHMITTRalph SchmittChief Executive Officer and Director 2




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EXHIBIT INDEX
 ExhibitNumber
    
    Description2.1
    
    Agreement and Plan of Reorganization dated October 21, 1999
by and among the Company, Calogic, CAT Acquisition
Corporation I and the other signatories thereto (previously
filed as Exhibit 2.1 to the Companys Form 8-K filed on
December 8, 1999 and incorporated herein by reference)2.2
    
    Amendment No. 1 to the Agreement and Plan of Reorganization
dated November 23, 1999 by and among the Company, Calogic,
CAT Acquisition Corporation I and the other signatories
thereto (previously filed as Exhibit 2.2 to the Companys
Form 8-K filed on December 8, 1999 and incorporated herein
by reference)3.1
    
    Amended and Restated Certificate of Incorporation
(incorporated herein by reference from the Companys
Registration Statement on Form 8-A filed with the
Securities and Exchange Commission on October 28, 2003)3.2
    
    Bylaws (incorporated herein by reference from the Companys
Registration Statement on Form 8-A filed with the
Securities and Exchange Commission on October 28, 2003)4.2
    
    Form of Indemnification Agreement for directors and
officers (filed as Exhibit 4.2 to the Companys
Registration Statement on Form S-1, File No. 333-1328, and
incorporated herein by reference)10.1**
    
    1988 Non-Statutory Stock Option Plan (filed as Exhibit 10.1
to the Companys Registration Statement on Form S-1, File
No. 333-1328, and incorporated herein by reference)10.2**
    
    1991 Non-Statutory Stock Option Plan (filed as Exhibit 10.2
to the Companys Registration Statement on Form S-1, File
No. 333-1328, and incorporated herein by reference)10.3**
    
    1993 Stock Option and Incentive Plan (filed as Exhibit 10.3
to the Companys Registration Statement on Form S-1, File
No. 333-1328, and incorporated herein by reference)10.4**
    
    1994 Stock Option and Incentive Plan (filed as Exhibit 10.4
to the Companys Registration Statement on Form S-1, File
No. 333-1328, and incorporated herein by reference)10.5**
    
    1996 Incentive Stock Option Plan (filed as Exhibit 10.5 to
the Companys Registration Statement on Form S-1, File No.
333-1328, and incorporated herein by reference)10.6
    
    1996 Non-Employee Director Stock Option Plan (filed as
Exhibit 10.6 to the Companys Registration Statement on
Form S-1, File No. 333-1328, and incorporated herein by
reference)10.7**
    
    1996 Employee Stock Purchase Plan (filed as Exhibit 10.7 to
the Companys Registration Statement on Form S-1, File No.
333-1328, and incorporated herein by reference)10.8**
    
    Employment Agreement dated August 19, 2002 by and between
the Company and Walid Maghribi (filed as Exhibit 99.1 to
the Companys 8K filed on August 23, 2002, and incorporated
herein by reference)10.9**
    
    Employment Agreement, as of the 14th day of May, 1999,
between the Company and James E. Donegan (filed as Exhibit
10.2 to the Companys Quarterly Report on Form 10-Q for the
quarter ended July 3, 1999, and incorporated herein by
reference)10.10**
    
    Employment Agreement, as of the 14th day of May, 1999,
between the Company and Raymond W.B. Chow (filed as Exhibit
10.4 to the Companys Quarterly Report on Form 10-Q for the
quarter ended July 3, 1999, and incorporated herein by
reference)10.11
    
    Form of Sales Representative Agreement (filed as Exhibit
10.15 to the Companys Registration Statement on Form S-1,
File No. 333-1328, and incorporated herein by reference)10.12
    
    Form of Sales Representative Agreement (previously filed
as an exhibit to the Companys Annual Report on Form 10-K
for the year ended December 31, 1998 and incorporated
herein by reference)10.13**
    
    1997 Incentive Stock Option Plan (filed as Appendix A to
the Companys definitive Proxy Statement for the Special
Meeting In Lieu Of Annual Meeting Of Shareholders held May
30, 1997 and incorporated herein by reference)10.14**
    
    Sipex Corporation 1999 Stock Plan (filed as Appendix A to
the Companys Definitive Proxy Statement on Schedule 14A,
No. 1000-27897, and incorporated herein by reference)10.15*
    
    License Agreement between Timex Corporation and Sipex
Corporation dated July 1, 1997 (previously filed as an
Exhibit to the Companys Annual Report on Form 10-K for the
year ended December 31, 1997, and incorporated herein by
reference)
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ExhibitNumber
    
    Description10.16**
    
    Employment Agreement, dated as of the 9th day of August,
1999 between the Company and Stephen E. Parks (filed as
Exhibit 10.1 to the Companys Quarterly Report on Form 10-Q
for the quarter ended July 3, 1999, and incorporated herein
by reference)10.17**
    
    2000 Non-Qualified Stock Option Plan (filed as an exhibit
to the Companys Annual Report on Form 10-K for the year
ended December 31, 2000, and incorporated herein by
reference)10.18**
    
    2002 Nonstatutory Stock Option Plan (filed as Exhibit 4.3
to the Companys Registration Statement on Form S-8, File
No. 73880, and incorporated herein by reference)10.19
    
    Deed of Reconveyance and Termination of Lease (filed as
Exhibit 10.2 to the Companys Quarterly Report on Form 10-Q
for the quarter ended June 30, 2001, and incorporated
herein by reference)10.20**
    
    Employment Agreement dated February 2, 2003 by and between
the Company and Phillip A. Kagel (filed as an Exhibit to
the Companys Annual report on Form 10-K for the year ended
December 31, 2002, and incorporated herein by reference)10.21**
    
    Employment Agreement dated September 11, 2002 by and
between the Company and Joseph T. Rauschmayer (filed as an
Exhibit to the Companys Annual report on Form 10-K for the
year ended December 31, 2002, and incorporated herein by
reference)10.22**
    
    Employment Agreement dated August 23, 2002 by and between
the Company and Kevin Plouse (filed as an Exhibit to the
Companys Annual report on Form 10-K for the year ended
December 31, 2002, and incorporated herein by reference)10.23
    
    Securities Purchase Agreement dated as of September 27,
2002, by and between the Company and S&F Financial
Holdings, Inc. (filed as Exhibit 99.2 to the Companys 8-K
filed on October 1, 2002, and incorporated herein by
reference)10.24
    
    Sipex Corporation 5.75% Convertible Secured Note due 2007
(filed as Exhibit 99.3 to the Companys 8-K filed on
October 1, 2002, and incorporated herein by reference).10.25
    
    Warrant to purchase 900,000 shares of common stock issued
to S&F Financial Holdings, Inc. (filed as Exhibit 99.4 to
the Companys 8-K on October 1, 2002, and incorporated
herein by reference)10.26
    
    Deed of Trust with Assignment of Rents dated as of
September 27, 2002, between the Company, First America
Title Insurance Company and S&F Financial Holdings, Inc.
(filed as Exhibit 99.5 to the Companys 8-K on October 1,
2002, and incorporated herein by reference)10.27
    
    Worldwide Authorized Distributor Market Price Agreement
dated July 22, 1993, by and between the Company and Future
Electronics Incorporated (filed as an Exhibit to the
Companys Annual report on Form 10-K for the year ended
December 31, 2002, and incorporated herein by reference)10.28
    
    Addendum A dated February 7, 2003 to Worldwide Authorized
Distributor Market Price Agreement dated July 22, 1993, by
and between the Company and Future Electronics Incorporated
(filed as an Exhibit to the Companys Annual report on Form
10-K for the year ended December 31, 2002, and incorporated
herein by reference)10.29
    
    Securities Purchase Agreement dated as of May 27, 2003, by
and between the Company and Alonim Investments Inc.
(previously filed as Exhibit 99.1 to the Companys Form 8-K
filed on May 29, 2003 and incorporated herein by reference)10.30
    
    Form of Company Convertible Secured Note to be issued to
Alonim Investments Inc. (previously filed as Exhibit 99.1
to the Companys Form 8-K filed on May 29, 2003 and
incorporated herein by reference)10.31
    
    Form of Registration and Standstill Agreement by and
between the Company and Alonim Investments Inc., and its
affiliates which are signatories thereto, namely: Future
Electronics Inc., and S&F Financial Holdings Inc.
(previously filed as Exhibit 99.1 to the Companys Form 8-K
filed on May 29, 2003 and incorporated herein by reference)10.32
    
    Form of Voting Agreement by and between the Company and
Alonim Investments Inc. (previously filed as Exhibit 99.1
to the Companys Form 8-K filed on May 29, 2003 and
incorporated herein by reference)10.33
    
    Form of Security Agreement by and between the Company and
Alonim Investments Inc. (previously filed as Exhibit 99.1
to the Companys Form 8-K filed on May 29, 2003 and incorporated herein by reference)10.34
    
    Form of Deed of Trust to be issued to Alonim Investments
Inc. (previously filed as Exhibit 99.1 to the Companys
Form 8-K filed on May 29, 2003 and incorporated herein by
reference)10.35
    
    Modification Agreement dated as of December 23, 2003 by and
among the Company and Rodfre Lending LLC and certain of its
affiliates (previously filed as Exhibit 99.1 to the
Companys Form 8-K filed on December 24, 2003)
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ExhibitNumber
    
    Description10.36
    
    Separation Agreement and Release as of 12/17/04 (previously
filed as Exhibit 99.2 to the Companys Form 8-K filed on
12/23/04 and incorporated herein by reference) with Mr.
Maghribi the former President and Chief Executive Officer
of Sipex and a former member of the Board of Directors of
Sipex10.37
    
    Letter agreement as of 12/17/04 (previously filed as
Exhibit 99.3 to the Companys Form 8-K filed on 12/23/04
and incorporated herein by reference) concerning the terms
of Mr. McBurnies employment with Sipex10.38
    
    Letter agreement as of 6/7/05 (previously filed as Exhibit
99 to the Companys Form 8-K filed on 6/30/05 and
incorporated herein by reference) concerning the terms of
the newly appointed Chief Executive Officer Ralph Schmitt10.39
    
    Loan and Security Agreement as of 7/21/05, (previously
filed as Exhibit 99.3 to the Companys Form 8-K filed on
7/25/05 and incorporated herein by reference) with Silicon
Valley Bank10.40
    
    Bonus plan as of August 29, 2005, (previously filed as
Exhibit 99.1 to the Companys Form 8-K filed on 9/2/05 and
incorporated herein by reference) for an executive bonus
plan for the remainder of 2005 for certain of its officers.10.41
    
    Separation Agreement and General Release as of 9/2/05
(previously filed as Exhibit 10.1 to the Companys Form 8-K
filed on 9/2/05 and incorporated herein by reference) with
Joseph T. Rauschmayer, Senior Vice President of Operations.10.42
    
    Grant of options (previously filed in the Companys Form
8-K filed on 9/25/05 and incorporated herein by reference)
to Mr. Wallin CFO and Mr. Hawron Sr. VP World Wide Sales10.43
    
    Separation Agreement and General Release as of 4/26/05
(previously filed as Exhibit 10.1 to the Companys Form 8-K
filed on 9/15/05 and incorporated herein by reference) with
Kevin Plouse10.44
    
    Letter agreement as of 9/12/05 (previously filed as Exhibit
10.1 to the Companys Form 8-K filed on 9/23/05 and
incorporated herein by reference) with Mr. Edward Lam
joining Sipex as the new Senior Vice President of Marketing
and Business Development.10.45
    
    Letter agreement as of 10/7/05 (previously filed as Exhibit
10.1 to the Companys Form 8-K filed on 10/12/05 and
incorporated herein by reference) with Joel Camarda joining
Sipex as Senior Vice President of Operations10.46
    
    Amendment No. 1 as of 10/7/05, (previously filed as Exhibit
10.1 to the Companys Form 8-K filed on 10/7/05 and
incorporated herein by reference) to the Loan and Security
Agreement with Silicon Valley Bank, dated July 21, 2005.10.47
    
    Amendment No. 2 as of 11/10/05, (previously filed as
Exhibit 10.1 to the Companys Form 8-K filed on 11/16/05
and incorporated herein by reference) to the Loan and
Security Agreement with Silicon Valley Bank, dated July 21,
2005.21.1
    
    Subsidiaries of the Company (previously filed as an exhibit
to the Companys Annual report on Form 10-K for the year
ended December 31, 2000, and incorporated herein by
reference.23.1
    
    Consent of Independent Registered Public Accounting Firm31.1
    
    Certification of Chief Executive Officer pursuant to
Section 302(a) of the Sarbanes-Oxley Act of 200231.2
    
    Certification of Chief Financial Officer pursuant to
Section 302(a) of the Sarbanes-Oxley Act of 200232.1
    
    Certification of Chief Executive Officer pursuant to 18
U.S.C section 1350, as adopted pursuant to Section 906 of
the Sarbanes-Oxley Act of 200232.2
    
    Certification of Chief Financial Officer pursuant to 18
U.S.C section 1350, as adopted pursuant to Section 906 of
the Sarbanes-Oxley Act of 2002
 
 *
    
    Confidential treatment as to certain portions has been requested pursuant to Rule 24b-2
promulgated under the Securities Exchange Act of 1934, as amended.**
    
    The Exhibits identified above with an asterisk (*) are management contracts or compensatory
plans or arrangements. 5