Exhibit 10.3

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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AMENDMENT NO. 1 TO MEMORANDUM OF UNDERSTANDING FOR TRANSFER PRICING AND ROYALTY CALCULATION

This amendment (“Amendment No. 1”) is entered into as of April __, 2011 and effective as of January 1, 2011 (the “Amendment Effective Date”) by and between Codexis, Inc., a Delaware corporation, having a place of business at 200 Penobscot Dr., Redwood City, CA 94063 (“Codexis”) and Arch Pharmalabs Limited, a corporation organized and existing under the laws of India having a place of business at H wing, 4^th Floor, Tex Centre, Chandivali, Mumbai, 400072, India (“Arch”).

WHEREAS, Arch and Codexis are parties to that certain Enzyme and Product Supply Agreement, effective as of February 16, 2010 (the “EPSA”) and the Memorandum of Understanding for Transfer Pricing and Royalty Calculation related thereto (the “MOU”); and

WHEREAS, the parties desire to amend the MOU to modify Arch’s manufacturing costs as set forth herein.

NOW, THEREFORE, in consideration of the premises and mutual covenants contained in this Amendment, the parties agree as follows:

1. Definitions. The capitalized terms used in this Amendment shall have the meanings assigned to such terms in the MOU, unless otherwise defined herein.

2. Amendment. Arch and Codexis agree that the MOU shall be amended in the manner set forth below:

Notwithstanding anything to the contrary, combined Direct Labor Expenses set forth in Paragraph B(ii), Indirect Expenses set forth in Paragraph C, and Overhead Expenses set forth in Paragraph D shall not, in respect of each Product, exceed the following amounts:

[*] Certain information in this document has been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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The amounts set forth in the above table are subject to quarterly review by the Parties pursuant to Section 3.3 of the MOU.

3. Ratification; Conflict. Except as otherwise expressly set forth in this Amendment, all of the terms and conditions of the EPSA and MOU shall remain in full force and effect. In the event of any conflict between the terms of this Amendment and the terms of the EPSA and MOU, the terms of this Amendment shall control.

4. Counterparts. This Amendment may be signed in one (1) or more counterparts, each of which will be deemed an original but all of which together will constitute one and the same instrument.

IN WITNESS WHEREOF, a duly authorized representative of each party has executed this Amendment as of the dates identified below, but the Amendment shall become effective on the Amendment Effective Date.