**EXHIBIT 31.1**

 

**CERTIFICATION**

 

I,Paul Goddard, certify that:

 

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

 

2.     Based on my knowledge, this report does notcontain 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 officer andI are responsible for establishing and maintaining disclosure controls andprocedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e))and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and15d-15(f)) 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 over financialreporting, or caused such internal control over financial reporting to bedesigned under our supervision, to provide reasonable assurance regarding thereliability of financial reporting and the preparation of financial statementsfor external purposes in accordance with generally accepted accounting principles;

 

c)              Evaluated the effectiveness of the registrant’sdisclosure controls and procedures and presented in this report our conclusionsabout the effectiveness of the disclosure controls and procedures, as of theend of the period covered by this report based on such evaluation; and

 

d)             Disclosed in this report any change in theregistrant’s internal control over financial reporting that occurred during theregistrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarterin the case of an annual report) that has materially affected, or is reasonablylikely to materially affect, the registrant’s internal control over financialreporting; and

 

5.     The registrant’s other certifying officer andI have disclosed, based on our most recent evaluation of internal control overfinancial reporting, to the registrant’s auditors and the audit committee ofthe 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:  November 13, 2009 | By:    | /s/  Paul Goddard                                              |
|-------------------------------|--------|----------------------------------------------------------------|
|                          |   |   Paul  Goddard, Ph.D.                               |
|                          |   |   Chairman  of the Board and Chief Executive Officer |

 

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