Main articles: Development of the Old Testament canon and Development of the New Testament canon

The Old Testament canon entered into Christian use in the Greek Septuagint translations and original books, and their differing lists of texts. In addition to the Septuagint, Christianity subsequently added various writings that would become the New Testament. Somewhat different lists of accepted works continued to develop in antiquity. In the fourth century a series of synods produced a list of texts equal to the39-to-46-book canon of the Old Testament and to the 27-book canon of the New Testament that would be subsequently used to today, most notably the Synod of Hippo in AD 393. Also c. 400, Jerome produced a definitive Latin edition of the Bible (see Vulgate), the canon of which, at the insistence of the Pope, was in accord with the earlier Synods. With the benefit of hindsight it can be said that this process effectively set the New Testament canon, although there are examples of other canonical lists in use after this time. A definitive list did not come from an Ecumenical Council until the Council of Trent (1545–63)

During the Protestant Reformation, certain reformers proposed different canonical lists than what was currently in use. Though not without debate, see Antilegomena, the list of New Testament books would come to remain the same; however, the Old Testament texts present in the Septuagint, but not included in the Jewish canon, fell out of favor. In time they would come to be removed from most Protestant canons. Hence, in a Catholic context these texts are referred to as deuterocanonical books, whereas in a Protestant context they are referred to as Apocrypha, the label applied to all texts excluded from the biblical canon which were in the Septuagint. It should also be noted, that Catholics and Protestants both describe certain other books, such as the Acts of Peter, as apocryphal.

Thus, the Protestant Old Testament of today has a 39-book canon—the number varies from that of the books in the Tanakh (though not in content) because of a different method of division—while the Roman Catholic Church recognizes 46 books as part of the canonical Old Testament. The term "Hebrew Scriptures" is only synonymous with the Protestant Old Testament, not the Catholic, which contains the Hebrew Scriptures and additional texts. Both Catholics and Protestants have the same 27-book New Testament Canon.