**EXHIBIT 31.1**

 

**CERTIFICATION**

 

I,Paul Goddard, certify that:

 

1.     I have reviewed thisquarterly report on Form 10-Q of ARYx Therapeutics, Inc.;

 

2.     Based on my knowledge, thisreport does not contain any untrue statement of a material fact or omit tostate a material fact necessary to make the statements made, in light of thecircumstances under which such statements were made, not misleading withrespect to the period covered by this report;

 

3.     Based on my knowledge, thefinancial statements, and other financial information included in this report,fairly present in all material respects the financial condition, results ofoperations and cash flows of the registrant as of, and for, the periodspresented in this report;

 

4.     The registrant’s othercertifying officer and I are responsible for establishing and maintainingdisclosure controls and procedures (as defined in Exchange ActRules 13a-15(e) and 15d-15(e)) and internal control over financialreporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f))for the registrant and have:

 

a)     Designed such disclosurecontrols and procedures, or caused such disclosure controls and procedures tobe designed under our supervision, to ensure that material information relatingto the registrant, including its consolidated subsidiaries, is made known to usby others within those entities, particularly during the period in which thisreport is being prepared;

 

b)    Designed such internalcontrol over financial reporting, or caused such internal control over financialreporting to be designed under our supervision, to provide reasonable assuranceregarding the reliability of financial reporting and the preparation offinancial statements for external purposes in accordance with generallyaccepted accounting principles;

 

c)     Evaluated the effectivenessof the registrant’s disclosure controls and procedures and presented in thisreport our 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 anychange in the registrant’s internal control over financial reporting thatoccurred during the registrant’s most recent fiscal quarter (the registrant’sfourth fiscal quarter in the case of an annual report) that has materiallyaffected, or is reasonably likely to materially affect, the registrant’sinternal control over financial reporting; and

 

5.     The registrant’s othercertifying officer and I have disclosed, based on our most recent evaluation ofinternal control over financial reporting, to the registrant’s auditors and theaudit committee of the registrant’s board of directors (or persons performingthe equivalent functions):

 

a)     All significant deficienciesand material weaknesses in the design or operation of internal control overfinancial reporting which are reasonably likely to adversely affect theregistrant’s ability to record, process, summarize and report financialinformation; and

 

b)    Any fraud, whether or notmaterial, that involves management or other employees who have a significantrole in the registrant’s internal control over financial reporting.

 

 
| Date:  November 15, 2010 | By:    | /s/  Paul Goddard                                  |
|--------------------------|--------|----------------------------------------------------|
|                     |   | Paul  Goddard, Ph.D.                               |
|                     |   | Chairman  of the Board and Chief Executive Officer |

 

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