Presbyterian churches firmly reject the inclusion of the Deuterocanonical books (also called the Apocrypha) — including Tobit, Judith, Wisdom of Solomon, Sirach (Ecclesiasticus), Baruch, 1-2 Maccabees, and additions to Esther and Daniel — in the biblical canon. The Westminster Confession of Faith (Chapter I, Section 3) explicitly states that 'the books commonly called Apocrypha, not being of divine inspiration, are no part of the canon of the Scripture; and therefore are of no authority in the church of God, nor to be any otherwise approved, or made use of, than other human writings.' This represents a clear Protestant stance, distinguishing Presbyterian churches from Roman Catholic and Eastern Orthodox traditions that include these books.

The Presbyterian argument for their exclusion rests on several grounds: the books were not included in the Hebrew Bible; they were composed after the close of the Hebrew prophecies; they are not cited as Scripture in the New Testament; and they lack the attestation from the broader Christian tradition regarding their divine inspiration. While these books may have historical and devotional value and can be read for instruction and edification, they are not treated as authoritative for doctrine or ethics. The 66-book canon (39 Old Testament books and 27 New Testament books) is understood as the complete and sufficient revelation of God's will.