AMENDMENT NO. 1 TO

SECURITIES PURCHASE AGREEMENT

AMENDMENT NO. 1, dated as of May 24, 2006 (this “Amendment”), to the Securities
Purchase Agreement, dated as of May 16, 2006 (the “Purchase Agreement”), by and
among Sipex Corporation, a Delaware corporation (the “Company”), and the Buyers
listed on the Schedule of Buyers attached thereto as Exhibit A (each a “Buyer”
and collectively, the “Buyers”). Each capitalized term used and not otherwise
defined herein shall have the meaning assigned to such term in the Purchase
Agreement.

WHEREAS, pursuant to the Purchase Agreement, the Company sold to the Buyers, and
each Buyer has severally purchased from the Company, the principal amount of
Notes and number of Warrants set forth opposite their respective names on
Exhibit A to the Purchase Agreement;

WHEREAS, the Company and the Buyers desire to modify the Purchase Agreement in
accordance with the provisions of Section 9(f) thereof; and

WHEREAS, the undersigned represent Investors holding at least 66 2/3% of the
Conversion Shares and Warrant Shares, determined as if all of the Notes held by
Buyers then outstanding have been converted into Conversion Shares and all
Warrants then outstanding have been exercised for Warrant Shares without regard
to any limitations on the conversion of the Notes or on the exercise of the
Warrants.

NOW, THEREFORE, in consideration of the mutual agreements herein contained and
other good and valuable consideration, the sufficiency and receipt of which are
hereby acknowledged, the parties hereto agree as follows:

Section 1. Amendments to the Purchase Agreement.

(a) Section 4 of the Purchase Agreement shall be amended to add Section 4(aa)
which shall read as follows:

DTC Settlement. The Company will use its reasonable best efforts to make the
Notes and Warrants, other than the Notes and Warrants issued to Rodfre Holdings
LLC, eligible to be registered for settlement through DTC no later than fifteen
(15) days following the satisfaction of the Exchange Act Filing Condition (as
defined in the Indenture).

Section 2. Acknowledgement of Scrivener’s Error. The parties hereby acknowledge
that the inclusion of the “Acknowledged and Agreed” signature block for Piper
Jaffray & Co. was a scrivener’s error and that Piper Jaffray’s acknowledgement
was unnecessary for the execution of the Purchase Agreement.

Section 3. Governing Law. All questions concerning the construction, validity,
enforcement and interpretation of this Amendment shall be governed by the
internal laws of the State of New York, without giving effect to any choice of
law or conflict of law provision or rule (whether of the State of New York or
any other jurisdictions) that would cause the application of the laws of any
jurisdictions other than the State of New York.

Section 4. Counterparts. This Amendment may be executed in identical
counterparts, each of which shall be deemed an original but all of which shall
constitute one and the same agreement. This Amendment, once executed by a party,
may be delivered to the other parties hereto by facsimile transmission of a copy
of this Agreement bearing the signature of the party so delivering this
Amendment.

Section 5. Headings. The headings of this Amendment are for convenience of
reference only and shall not limit or otherwise affect the meaning thereof.

Section 6. Effect of Amendment. Except as expressly amended by this Amendment,
the Purchase Agreement shall remain in full force and effect as the same was in
effect immediately prior to the effectiveness of this Amendment. All references
in the Purchase Agreement to “this Agreement” shall be deemed to refer to the
Purchase Agreement as amended by this Amendment.

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IN WITNESS WHEREOF, the parties hereto have caused this Amendment to be duly
executed by their respective authorized officers as of the day and year first
above written.

     
SIPEX CORPORATION
By:
 
   /s/    Ralph Schmitt                                  
 
   
 
  Name: Ralph Schmitt
Title: President and Chief Executive Officer

    BUYERS

(print full legal name of Buyer)

By:

(signature of authorized representative)

Name:

Its:

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IN WITNESS WHEREOF, the parties hereto have caused this Amendment to be duly
executed by their respective authorized officers as of the day and year first
above written.

     
SIPEX CORPORATION
By:
 
                                     
 
   
 
  Name: Ralph Schmitt
Title: President and Chief Executive Officer

BUYERS

Rodfre Holding LLC

(print full legal name of Buyer)

By: /s/ Joe Prudente, Manager and Director

(signature of authorized representative)

Name: Joe Prudente, Manager and Director

Its:

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IN WITNESS WHEREOF, the parties hereto have caused this Amendment to be duly
executed by their respective authorized officers as of the day and year first
above written.

     
SIPEX CORPORATION
By:
 
                                     
 
   
 
  Name: Ralph Schmitt
Title: President and Chief Executive Officer

BUYERS

Quantum Partners LDC

(print full legal name of Buyer)

By: /s/ Jay A. Schoenfarber

(signature of authorized representative)

Name: Jay A Schoenfarber

Its: Attorney-in-Fact

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IN WITNESS WHEREOF, the parties hereto have caused this Amendment to be duly
executed by their respective authorized officers as of the day and year first
above written.

     
SIPEX CORPORATION
By:
 
                                     
 
   
 
  Name: Ralph Schmitt
Title: President and Chief Executive Officer

BUYERS

THE NORTHWESTERN MUTUAL LIFE INSURANCE COMPANY

(print full legal name of Buyer)

By: /s/ Jerome R. Baier

(signature of authorized representative)

Name: Jerome R. Baier

Its: Authorized Representative

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IN WITNESS WHEREOF, the parties hereto have caused this Amendment to be duly
executed by their respective authorized officers as of the day and year first
above written.

     
SIPEX CORPORATION
By:
 
                                     
 
   
 
  Name: Ralph Schmitt
Title: President and Chief Executive Officer

BUYERS

THE NORTHWESTERN MUTUAL LIFE INSURANCE COMPANY FOR ITS GROUP ANNUITY SEPARATE
ACCOUNT

(print full legal name of Buyer)

By: /s/ Jerome R. Baier

(signature of authorized representative)

Name: Jerome R. Baier

Its: Authorized Representative

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