**EXHIBIT 31.1**

 

**CERTIFICATION**

 

I, Paul Goddard, certifythat:

 

1.               I have reviewed this quarterly report on Form 10-Qof ARYx Therapeutics, Inc.;

 

2.               Based on my knowledge, this report doesnot contain any untrue statement of a material fact or omit to state a materialfact necessary to make the statements made, in light of the circumstances underwhich such statements were made, not misleading with respect to the periodcovered by this report;

 

3.               Based on my knowledge, the financialstatements, and other financial information included in this report, fairlypresent in all material respects the financial condition, results of operationsand cash flows of the registrant as of, and for, the periods presented in thisreport;

 

4.               The registrant’s other certifying officerand I are responsible for establishing and maintaining disclosure controls andprocedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e))for the registrant and have:

 

a)              Designed such disclosure controls andprocedures, or caused such disclosure controls and procedures to be designedunder our supervision, to ensure that material information relating to theregistrant, including its consolidated subsidiaries, is made known to us byothers within those entities, particularly during the period in which thisreport is being prepared;

 

b)             Designed such internal control overfinancial reporting, or caused such internal control over financial reportingto be designed under our supervision, to provide reasonable assurance regardingthe reliability of financial reporting and the preparation of financialstatements for external purposes in accordance with generally acceptedaccounting principles;

 

c)              Evaluated the effectiveness of theregistrant’s disclosure controls and procedures and presented in this reportour conclusions about the effectiveness of the disclosure controls andprocedures, as of the end of the period covered by this report based on suchevaluation; and

 

d)             Disclosed in this report any change inthe registrant’s internal control over financial reporting that occurred duringthe registrant’s most recent fiscal quarter (the registrant’s fourth fiscalquarter in the case of an annual report) that has materially affected, or isreasonably likely to materially affect, the registrant’s internal control overfinancial reporting; and

 

5.               The registrant’s other certifying officerand I have disclosed, based on our most recent evaluation of internal controlover financial reporting, to the registrant’s auditors and the audit committeeof registrant’s board of directors (or persons performing the equivalentfunctions):

 

a)              All significant deficiencies and materialweaknesses in the design or operation of internal control over financialreporting which are reasonably likely to adversely affect the registrant’sability to record, process, summarize and report financial information; and

 

b)             Any fraud, whether or not material, thatinvolves management or other employees who have a significant role in theregistrant’s internal control over financial reporting.

 

 
| Date: May 14, 2009 | By:    | /s/ Paul Goddard, Ph.D.                            |
|-------------------------|--------|----------------------------------------------------|
|                    |   | Paul  Goddard, Ph.D.                               |
|                    |   | Chairman  of the Board and Chief Executive Officer |

 

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