Short answer. Dozens, in distinct categories, cut for different reasons over centuries. The Old Testament apocrypha (Tobit, Wisdom, 1-2 Maccabees) stay in Catholic Bibles but were dropped by Protestants. The pseudepigrapha (1 Enoch, Jubilees) were quoted as scripture early, then aged out. The Gnostic gospels (Thomas, Mary) were branded heretical. No single council "deleted" them: it was a long sift over date, theology, and use.
There is no one "Bible", so "left out" depends on whose canon
The first honest move is to notice that the question hides a fork: different communities ended up with different Bibles, so a book "left out" of one is scripture in another. Roman Catholic and Eastern Orthodox Old Testaments include the deuterocanonical books (Tobit, Judith, Wisdom of Solomon, Sirach, Baruch, and 1-2 Maccabees) that Protestant Bibles, following Jerome's preference for the Hebrew canon, relegated to a separate "Apocrypha" section or dropped entirely (Metzger, The Canon of the New Testament, 1987). The Ethiopian Orthodox canon is broader still, retaining 1 Enoch and Jubilees as scripture to this day. So "left out of the Bible" usually means left out of the Protestant canon that became default in the English-speaking world. As Bart Ehrman frames it in Lost Christianities (2003), the canon we inherited is the paperwork of the side that won, a real historical outcome, not a verdict handed down from a mountain. The point for an honest reader: exclusion is plural, and the reasons differ book by book.
The Old Testament apocrypha: cut by translation politics, not heresy
The deuterocanonical books were not excluded for teaching anything monstrous; they were excluded over a dispute about which text counted. These works (composed mostly in the last two centuries BCE) survived in the Greek Septuagint, the Bible the earliest Christians actually read, but most were absent from the later rabbinic Hebrew canon. When Jerome translated the Latin Vulgate around 400 CE, he flagged the books found only in Greek as useful for edification but not for establishing doctrine (Metzger, 1987). That distinction lay mostly dormant until the Reformation, when Protestants pressed Jerome's logic and demoted them, and the Council of Trent (1546) responded by formally affirming them as canonical for Catholics. The stakes were doctrinal in hindsight: 2 Maccabees 12 depicts prayer and atonement for the dead, a proof-text for purgatory, and the developed afterlife and bodily-resurrection hope in 2 Maccabees 7 and the Wisdom of Solomon mark a real theological shift (Levenson, Resurrection, 2006). These books were a bridge, not a heresy, which is why their exclusion looks more like a translation-and-authority quarrel than a suppression.
1 Enoch and Jubilees: scripture that the canon outgrew
Some excluded books were not fringe at all: they were cited as authoritative and then quietly aged out. 1 Enoch is the clearest case. The New Testament Epistle of Jude (verses 14-15) quotes 1 Enoch by name as prophecy, and its "Watchers" myth (fallen angels descending in the days of Genesis 6 to corrupt humanity) shaped Second Temple thinking about the origin of evil and the demonic (VanderKam; Collins). The book of Jubilees, a retelling of Genesis and Exodus, was likewise treated as authoritative at Qumran, where copies turned up among the Dead Sea Scrolls. Both were eventually dropped by the rabbinic and proto-orthodox mainstreams (too entangled with an angelology and a 364-day solar calendar that the consolidating traditions moved away from) yet both were retained as canonical by the Ethiopian church. Here the honest reframe matters: a book quoted inside the New Testament can still end up outside the canon. That tells you canon was a moving boundary, sifted by later usage and theology, not a fixed list dropped intact from the start.
The Gnostic gospels: branded heretical, by named men, at datable moments
The texts most people picture when they hear "books left out of the Bible" are the later ones, the Coptic codices unearthed at Nag Hammadi in 1945, including the Gospel of Thomas, the Gospel of Philip, and (recovered separately) the Gospel of Mary. These were excluded for the hardest reason: theology. Around 180 CE the bishop Irenaeus, in Against Heresies, ruled such teachers out of bounds and insisted on four Gospels and only four (Pagels, The Gnostic Gospels, 1979; King, What Is Gnosticism?, 2003). Many of these works are also simply late (second-century compositions, not eyewitness records) which gave the proto-orthodox a defensible criterion beyond doctrine. The Gospel of Thomas, a sayings-collection ("the kingdom is inside of you, and it is outside of you," Saying 3, Lambdin translation), made the institution optional by locating salvation in inner knowing; the Gospel of Mary stages an argument over whether authority follows office or insight. Karen King's caution holds: "Gnosticism" is a contested umbrella term, assembled partly from the heresy-hunters' own insults, not a single rival church. These books were marginalized, but by argument, attrition, and eventually power, across generations.
So what were the real criteria?
Strip the legend away and three working tests recur in how early Christians sorted books (Metzger, 1987; Ehrman, 2003):
- Date and authorship. Apostolic origin counted; second-century works like Thomas failed the test (a real criterion, honestly applied).
- Theology ("rule of faith"). Books teaching a lesser Creator-god or a Jesus who only seemed human were ruled out, the proto-orthodox had genuine doctrinal reasons, not only turf (Pagels, 1979).
- Use. What congregations actually read in worship across many regions tended to stabilize as canon; locally-read books faded.
These criteria pulled against each other and produced different results in different churches, which is exactly why there is no single tidy list of "the books they removed."
Common questions
Why did Protestants remove books from the Bible?
The deuterocanonical books (Tobit, Judith, Wisdom of Solomon, Sirach, Baruch, and 1-2 Maccabees) were not excluded for teaching anything monstrous; they were excluded over a dispute about which text counted. They survived in the Greek Septuagint, the Bible the earliest Christians read, but most were absent from the later rabbinic Hebrew canon. When Jerome translated the Vulgate around 400 CE, he flagged the Greek-only books as useful for edification but not for establishing doctrine; the Reformers pressed that logic and demoted them. So this looks more like a translation-and-authority quarrel than a suppression.
Is the Book of Enoch in the Bible?
It depends on whose Bible. 1 Enoch was dropped by the rabbinic and proto-orthodox mainstreams, but it is retained as canonical by the Ethiopian church to this day. Notably, the New Testament Epistle of Jude (verses 14-15) quotes 1 Enoch by name as prophecy. That a book quoted inside the New Testament can still end up outside the canon tells you canon was a moving boundary, sifted by later usage and theology, not a fixed list dropped intact from the start.
Why were the Gnostic gospels left out of the Bible?
The Gnostic gospels (Thomas, Philip, Mary) were excluded for the hardest reason: theology. Around 180 CE the bishop Irenaeus, in Against Heresies, ruled such teachers out of bounds and insisted on four Gospels and only four. Many of these works are also simply late, second-century compositions rather than eyewitness records, which gave the proto-orthodox a defensible criterion beyond doctrine. They were marginalized by argument, attrition, and eventually power, across generations, not deleted at a single moment.
Is the Apocrypha the same as the Gnostic gospels?
No. They are distinct categories cut for different reasons. The Old Testament apocrypha (the deuterocanonical books) were excluded over a dispute about which text counted, a translation-and-authority quarrel, not heresy. The Gnostic gospels were branded heretical on grounds of theology and late date. Lumping them together obscures that exclusion was plural, and the reasons differ book by book.
This settles that exclusion was plural and gradual (different books cut for different reasons (translation politics, shifting theology, late date, heresy-hunting) across centuries) and does not settle that any one council "deleted" a secret true Bible. The canon was a contested boundary, drawn by named people at datable moments, not a conspiracy with a single switch.
Sources
Jude 14-15; Genesis 6; 2 Maccabees 7 and 12; Wisdom of Solomon; Gospel of Thomas, Saying 3; Bruce M. Metzger,* The Canon of the New Testament (1987); Bart D. Ehrman, Lost Christianities (2003); Elaine Pagels, The Gnostic Gospels (1979); Karen L. King, What Is Gnosticism? (2003); James VanderKam and John J. Collins on 1 Enoch and Jubilees; Jon D. Levenson, Resurrection and the Restoration of Israel *(2006).