Exhibit 31.1
CERTIFICATION
I, Alan Shaw, certify that:
| 1. | I have reviewed this Amendment No. 1 to the Quarterly Report of Codexis, Inc.; and |
| 2. | Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report. |
Date: October 28, 2011
| /s/ Alan Shaw |
| Alan Shaw |
| President and Chief Executive Officer |