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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2015-06-05</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001623919</issuerCik>
        <issuerName>EndoChoice Holdings, Inc.</issuerName>
        <issuerTradingSymbol>GI</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001643849</rptOwnerCik>
            <rptOwnerName>Rubey Kevin</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ENDOCHOICE HOLDINGS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>11810 WILLS ROAD</rptOwnerStreet2>
            <rptOwnerCity>ALPHARETTA</rptOwnerCity>
            <rptOwnerState>GA</rptOwnerState>
            <rptOwnerZipCode>30009</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>See remarks.</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common stock, par value $0.001 per share</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>41442</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Includes 17,992 shares of restricted common stock vesting in four equal annual installments beginning on January 21, 2014, 17,530 shares of restricted common stock vesting in four equal annual installments beginning on September 19, 2014 and 5,920 shares of restricted common stock vesting in four equal annual installments beginning on April 14, 2016.</footnote>
    </footnotes>

    <remarks>Chief Operating Officer</remarks>

    <ownerSignature>
        <signatureName>/s/ James B. Young, Jr., as attorney-in-fact</signatureName>
        <signatureDate>2015-06-05</signatureDate>
    </ownerSignature>
</ownershipDocument>
