Sheppard's alternatim hymn compositions, as with those of Tallis, follow a practice established in England more than a century previously whereby the even-numbered stanzas, set polyphonically, alternate with the plainsong melody. They are for between five and eight voices, and in all but a few cases the cantus firmus is in the top voice. It has been suggested that the two composers, the principal exponents of the genre at this time, may have collaborated to produce a scheme for Mary Tudor's Chapel Royal for the various seasons and feasts of the liturgical year. Certainly Sheppard's eighteen polyphonic hymns (of which two are sometimes attributed to Tallis), together with those by Tallis, provide an extensive range of such works for the Office. William Byrd and Robert White also contributed to the genre at this time while a number of alternatim settings for organ also survive, by Tallis, Redford and others, in which the odd- rather than even-numbered stanzas are worked.

Sheppard's hymns were written for the Sarum rite. Jesu, salvator saeculi, verbum is a Compline hymn for the period from Low Sun<utJ until Ascension Day while Deus tuorum militum is a Vespers hymn for the feast of a Martyr, except during the Christmas and Easter periods; it is specified also for the feast of St Stephen in the Roman liturgy.