Was the 66 book Bible being used by early Christians? Referring to the most widely used Protestant canon of exactly (and only) the content of these 66 books.
The answer is most certainly no.


The oldest complete Bible that we have is the Codex Vaticanus, dating to between 300 and 325.  It contains 68 books:  45 Old Testament books plus 23 New Testament books.  The Old Testament includes 2 Esdras (sometimes called "Ezra-Nehemiah"), Tobit, Judith, Wisdom, Sirach and the Psalms of Solomon.  The New Testament lacks 1 and 2 Timothy, Titus, Philemon, and Revelation.
The next oldest complete Bible we have is the Codex Sinaiticus, dating to between 330 and 360.  The Old Testament of the Sinaiticus manuscript is not complete, but it includes several deuterocanonical books:  2 Esdras, Sirach, Tobit, Judith, 1-4 Maccabees.  Assuming the Hebrew canon was complete, the Sinaiticus then would have contained over 45 Old Testament books.  Furthermore, Sinaiticus also included two New Testament books that were later excluded from the canon:  the Epistle of Barnabas and the Shepherd of Hermas.  Together then, New Testament and Old comprised over 74 books.
The first formal Bible canon was set at the 3rd Council of Carthage in 397.  Canon XXXIII of the Council established a 44 book Old Testament and a 27 book New Testament canon, bringing the total to 71 books. 
The very first Christian to introduce a New Testament canon was Marcion of Sinope (c 85-160). Marcion essentially rejected the Old Testament and accepted only the Gospel according to Luke and ten Pauline Epistles - essentially defining an 11-book Biblical canon.  Although Marcion was eventually condemned as a heretic and excommunicated, his movement persisted for at least 300 years.


These are a few examples of the discrepancies between the Bibles used by Christians in antiquity, all serving to illustrate that the number of books included was by no means stable.

A work of a 19th century Presbyterian theologian, Archibald Alexander, has been cited as an authority for the argument that early Christians only recognized the 39 books of the modern day Protestant Old Testament canon as authoritative.  In the book, Canon of the Old and New Testaments Ascertained, or The Bible Complete without the Apocrypha and Unwritten Traditions, regarding the deuterocanon, Alexander makes the claim "that these books were not received as canonical by the Christian Fathers, but were expressly declared to be apocryphal".  As evidence of this, he appeals to the authority of several Church Fathers and early Christian writers.  There are many weaknesses in his claims.  For example:


He states that Justin Martyr (100-165) "does not cite a single passage, in all his writings, from any apocryphal book."  By this logic, any book not quoted by Justin would be considered non-canonical.  A review of Schaff's index of Scriptures cited by Justin Martyr (from the Ante-Nicene Fathers series, vol.1) shows that Justin Martyr quoted from 24 Old Testament books and 13 New Testament books.  Does this imply that he held to a 37-book Bible canon?
Having cited Justin Martyr as an authority for ignoring the deuterocanon, he neglects to mention that Ireneaus of Lyon (130-202) - a contemporary of Justin Martyr and perhaps an even more authoritative Church Father - quotes from the Wisdom of Solomon and Sirach (Ecclesiasticus) in Against Heresies.
He quotes a list of Old Testament books given, according to Eusebius1, by Melito of Sardis (d. 180) that appears to exclude Esther, Lamentations (which some say is included in Jeremiah), and Nehemiah (which some say is included in Ezra) and may or may not include the Wisdom of Solomon (some say he was referring to "Proverbs" with the phrase ἣ καὶ Σοφία).  In all, Melito's list implies an Old Testament canon of between 36 and 39 books, depending on whether one considers Wisdom, Lamentations, and/or Nehemiah to have been included in the enumeration - with a total of 39 reached only with the inclusion of Wisdom.
He correctly quotes Origen as saying, "We should not be ignorant, that the canonical books are the same which the Hebrews delivered unto us, and are twenty-two in number, according to the number of letters of the Hebrew alphabet.”  He neglects to point out that Origen concluded his discussion of the Old Testament canon with the note, "And besides these there are the Maccabees"2 - which meant that Origen recognized between 41 and 44 books in the Old Testament (3 Maccabees and 4 Maccabees are not always enumerated in other Old Testament canons of the early Church).
He attributes a list from a work called The Synopsis of Sacred Scripture to Athanasius, though scholars generally agree that it was written by some clergyman in the 6th century.  This list also excludes Esther from the list of "canonical" books and instead places it with a list of "non-canonical" books. Further, he quotes only a part of the document. "Such are the books belonging to the Old Testament", it states, "including those which are canonical and those which are not canonical."  In addition to Esther, the list of "non-canonical" books given includes the Wisdom of Solomon, Sirach, Judith, and Tobit.  So depending on whether the "non-canonical" books are to be considered as part of the Old Testament or not, the Synopsis describes an Old Testament canon of either 38 or 43 books.
He again selectively quotes the work of another Church Father, Hilary of Poitiers (310-368), omitting the statement, "To this some add Tobit and Judith to make twenty-four books, according to the number of the Greek letters, which is the language used among Hebrews and Greeks gathered in Rome."3  Thus, Hilary describes an Old Testament canon of between 39 and 41 books.  
He states that "Jerome, in his Epistle to Paulinus, gives us a catalogue of the books of the Old Testament, exactly corresponding with that which Protestants receive: 'Which,' says he, 'we believe agreeably to the tradition of our ancestors, to have been inspired by the Holy Spirit.'"  He neglects to point out, however, that Jerome included Tobit, Judith, and Sirach in his Latin translation of the Bible (see "Prefaces to the Books of the Vulgate Version of the Old Testament" here)


Alexander goes on to look for support in some other patristic sources.  I have not bothered to go through the rest of these in detail.  Of these, however, his quote from John Chrysostom (c 349-407) is especially preposterous.  He misquotes Chrysostom as saying in his 4th Homily on Genesis:


  That all the divine books of the Old Testament were originally written in the Hebrew tongue, and that no other books were received.


What Chrysostom actually wrote was:


  All the sacred books of the Old Testament were originally written in Hebrew; everyone would agree with us on this.


Furthermore, Chrysostom in this very same Homily quotes the deuterocanonical book of Sirach (25:9), writing:


  Scripture says, remember, Blessed is the one that preaches to willing ears.


He also quotes from Wisdom (13:5) in the same homily.  In his homilies on Matthew alone, Chrysostom quotes 4 times from the Book of Wisdom, 18 times from Sirach, and twice from Baruch - all deuterocanonical books.  To maintain that he did not accept the deuterocanon as Scriptural is simply inexcusable.  In fact, one would be hard-pressed not to find Chrysostom citing the deuterocanon in any one of his 17 commentaries on the New Testament.

Please note that I am not addressing the question of whether the deuterocanon should or should not be included in Scripture.  I am simply pointing out that based on the writings of many respected Church Fathers and early Christian writers, the deuterocanon was generally considered to be part of Scripture, with varying degrees of acceptance (e.g. it was included in the Old Testament, but at a different level from the "Hebrew" Scriptures).  It's standing even among Jews can be called into question, as copies of Sirach and Tobit were found among the Dead Sea Scrolls (as was a copy of 1 Enoch).  All this points to the fact that even with the New Testament canon settled, early Christians did not uniformly and consistently - or perhaps not at all - recognize a 66-book Bible.



1. Eusebius, Church History, IV.26
2. Ibid., VI.25
3. Exposition on the Psalms XV