<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2008-11-14</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001410064</issuerCik>
        <issuerName>ARYx Therapeutics, Inc.</issuerName>
        <issuerTradingSymbol>ARYX</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001055951</rptOwnerCik>
            <rptOwnerName>ORBIMED ADVISORS LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>767 3RD AVENUE</rptOwnerStreet1>
            <rptOwnerStreet2>30TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10017</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001055949</rptOwnerCik>
            <rptOwnerName>ISALY SAMUEL D</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>767 THIRD AVE.</rptOwnerStreet1>
            <rptOwnerStreet2>30TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10017</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2008-11-14</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>1214646</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F4"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>3340139</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Common Stock Warrants (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>2.64</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2008-11-14</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>364395</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F4"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2008-11-14</value>
            </exerciseDate>
            <expirationDate>
                <value>2013-11-14</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>364395</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>364395</value>
                    <footnoteId id="F3"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The amount shown represents (i) 2,237,773 shares of Common Stock held directly by Caduceus Private Investments, LP (&quot;Caduceus&quot;), (ii) 46,580 shares of Common Stock held directly by OrbiMed Associates, LLC (&quot;Associates&quot;), and (iii) 1,055,786 shares of Common Stock held directly by UBS Juniper Crossover Fund, L.L.C. (&quot;Juniper&quot;), all of which are deemed to be affiliates of the Reporting Persons.</footnote>
        <footnote id="F2">OrbiMed Advisors LLC &quot;Advisors&quot;)is a registered adviser under the Investment Advisors Act of 1940,as amended,that acts as an investment adviser to certain collective investment funds which hold shares of the Issuer.  Samuel D. Isaly, a natural person, owns a controlling interest in Advisors and OrbiMed Capital GP I, LLC (&quot;Capital&quot;).Capital is the general partner of Caduceus. Advisors is the managing member of Associates and is a joint venture member of the investment adviser of Juniper with full trading discretion. Pursuant to certain agreements and relationships, Advisors and Capital have discretionary investment managment authority with respect to the assets of Caduceus, Associates, and Juniper. Such authority includes the power to vote and otherwise dispose of securities purchased by Caduceus, Associates and Juniper. The Reporting Persons disclaim beneficial ownership of all of these securities except to the extent of their respective pecuniary interest therein</footnote>
        <footnote id="F3">Consists of warrants to purchase (i) 244,131 shares held by Caduceus (ii) 5,082 shares held by Associates, and (iii) 115,182 shares held by Juniper, all of which are deemed to be affiliates of the Reporting Persons.</footnote>
        <footnote id="F4">These securities were purchased as part of a private placement transaction by the Issuer pursuant to the terms of a certain securities purchase agreement, dated November 11, 2008, a copy of which was filed as an exhibit to the Issuer's Current Report on Form 8-K filed on November 12, 2008. The combined purchase price of each share of common stock and each warrant to purchase 0.30 of a share of common stock issued in the private placement is $2.2375.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/Samuel D. Isaly, President</signatureName>
        <signatureDate>2008-11-18</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/Samuel D. Isaly</signatureName>
        <signatureDate>2008-11-18</signatureDate>
    </ownerSignature>
</ownershipDocument>
