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.
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.
The basic answer is "yes"; the early Christians and Protestants used the same books and considered them only inspired. For the most part, there was no dispute over the 27 books of the New Testament. The question really arose about the canon of the Old Testament.
We have at least two earliest commentaries that support the same Old Testament canon of Protestants at 39 books. The first is from Josephus and the second is from Melito.
After them, we also have Origen and Jerome, amongst others, who agree with the 39 books only as inspired. See this link for more.
The usefulness of Josephus is not only because he outlines what Protestants use, but also because he tells us why there was a difference in the books written after Artaxerxes; that is, there was no valid prophetic line. Artaxerxes figures into the 70 weeks of Daniel, suggesting completed, though not fulfilled, prophecy, until Messiah. Interestingly, even Maccabees itself will tell us that it is not inspired for exactly that reason; that is, there was no valid prophetic line at the time of its writing. See 1 Macc 4:46 and 14:41.
- For we have not an innumerable multitude of books among us, disagreeing from and contradicting one another, [as the Greeks have,] but only twenty-two books, which contain the records of all the past times; which are justly believed to be divine; and of them five belong to Moses, which contain his laws and the traditions of the origin of mankind till his death. This interval of time was little short of three thousand years; but as to the time from the death of Moses till the reign of Artaxerxes king of Persia, who reigned after Xerxes, the prophets, who were after Moses, wrote down what was done in their times in thirteen books. The remaining four books contain hymns to God, and precepts for the conduct of human life. It is true, our history hath been written since Artaxerxes very particularly, but hath not been esteemed of the like authority with the former by our forefathers, because there hath not been an exact succession of prophets since that time; and how firmly we have given credit to these books of our own nation is evident by what we do; for during so many ages as have already passed, no one has been so bold as either to add any thing to them, to take any thing from them, or to make any change in them; but it is become natural to all Jews immediately, and from their very birth, to esteem these books to contain Divine doctrines, and to persist in them, and, if occasion be willingly to die for them. Against Apion, Book 1, 8
From Artaxerxes until John the Baptist, the last recognized OT prophet, was the so-called "silent period" of about 400 years during which all God-inspired prophecy had been spoken until the start of the time when it was becoming fulfilled.
Melito's list is identical to the current Old Testament canon, except for excluding Esther. One potential reason Esther is not listed is because of its "touchy" nature. It's also interesting that Melito mentions "Old Testament", implying that at that very early stage circa 170 CE there was a "New Testament" (see Muratorian Fragment).
I [Melito] accordingly proceeded to the East, and went to the very spot where the things in question were preached and took place; and, having made myself accurately acquainted with the books of the Old Testament, I have set them down below, and herewith send you the list. Their names are as follows:— The five books of Moses—Genesis, Exodus, Leviticus, Numbers, Deuteronomy; Joshua,3623 Judges, Ruth, the four books of Kings, the two of Chronicles, the book of the Psalms of David, the Proverbs of Solomon, also called the Book of Wisdom, Ecclesiastes, the Song of Songs, Job, the books of the prophets Isaiah, Jeremiah, of the twelve contained in a single book, Daniel, Ezekiel, Esdras. From these I have made my extracts, dividing them into six books. Melito Recording
So, the idea was that for a book to be included in the Old Testament canon, it had to be written by or during the time of a valid prophet. This meant "God breathed". This criteria is exactly the same as for deciding which books should make up the New Testament (times of apostles). Obviously different denominations (Catholic, Orthodox, Protestant) disagree with the validity of a "God-only breathed" book and a secular book, but it is interesting that of the three, only Protestants esteem the Bible as more authoritative than man's writings or traditions.
The answer appears to be, "No." I would recommend you read this book: Where We Got the Bible: Our Debt to the Catholic Church by Bishop Henry Graham.
This next one I haven't read, but I often hear it recommended: Why Catholic Bibles are Bigger by Gary Michuta.
The answer is 'no' because Protestants beginning with Martin Luther began ignoring some of the Bible that didn't agree with their theology. As I recall, Graham's book examines history and determines that the early Christians used the books canonized by the Catholic Church today. I have been told that Michuta discusses this history in greater detail.
The modern Protestant Bible is comprised of 39 books in the Old Testament and 27 books in the New Testament, for a total of 66 books.
Your question is: "Was the 66 book Bible being used by early Christians?", with the clarification "Referring to the most widely used Protestant canon of exactly (and only) the content of these 66 books."
The short answer is no. The modern Protestant canon was never used in a Christian bible until the English civil war in the 1640s. Not even the Reformers or early Protestants used the modern Protestant canon.
Don't just take my word for it, let us prove it by reviewing throughout history all the lists of canon we have, and noting how they diverged from the modern Protestant Bible.
Around 170 AD, Melito of Sardis gives an Old Testament list which excludes Lamentations, Nehemiah, and Esther (Eusebius' Ecclesiastical History, Book IV, Chapter 26, Section 14)
Also dating from around 170 AD, the Muratorian fragment gives a New Testament list which excludes James, 1 & 2 Peter, Hebrews, and 3 John and includes the Book of Wisdom.
Around 240 AD, Origen gives a New Testament list excluding Revelation (Homilies on Joshua, 7.1), and an Old Testament list for the Jews which excludes the 12 minor prophets and includes the Epistle of Jeremiah - part of the book of Baruch (Eusebius' Ecclesiastical History, Book VI, Chapter 25, Section 1-2).
Around 350 AD, Cyril of Jerusalem gives a New Testament list excluding Revelation, and an Old Testament list including the book of Baruch (Catechetical Lecture 4, sections 35-36).
Around 367 AD, Hilary of Poitiers gives an Old Testament list which includes the Epistle of Jeremiah - part of the book of Baruch, and notes that some accept Tobit and Judith (Expositions of the Psalms, 15).
Also around 367 AD, Athanasius in a letter gives the first full New Testament list comprising all 27 books. He also gives an Old Testament list, including Baruch and excluding Esther. He says Esther, the book of Wisdom, Sirach, Judith, Tobit, the Didache, and the Shepherd of Hermes were called non-Canon but profitable for instruction in the word of godliness (Letter 39).
Around 382 AD, the Council of Rome was held which gave the full New Testament list, and gave an Old Testament list including the full Deuterocanon (Tobit, Judith, 1 & 2 Maccabees, the Book of Wisdom, etc) (Decretum Gelasianum, Damasine List, Section II).
Around 385 AD, Epiphanius of Salamis gave an Old Testament list which included Baruch. He also noted two more books of disputed canonicity, Sirach and the Book of Wisdom - which he later on called 'divine writings'. (Panarion viii. 6 and Panarion lxxvi. 5
Around 390 AD, Gregory of Nazianzus gave a New Testament list excluding Revelation, and an Old Testament list excluding Esther (Concerning the Genuine Books of Divinely Inspired Scripture)
Also around 390 AD, Augustine gave the full New Testament list, and gave an Old Testament list including the full Deuterocanon (Tobit, Judith, 1 & 2 Maccabees, the Book of Wisdom, etc) (On Christian Doctrine, Book II, Chapter 8, Section 13).
Also around 390 AD, Jerome argues the Book of Wisdom, Sirach, Judith, Tobit, and 2 Maccabees should be placed among the Apocryphal writings (Prologue to the Books of the Kings).
Note that Jerome did not explicitly exclude Baruch. Indeed, later Jerome quotes from Baruch as a prophet (Letter 77, Section 4). It's reasonable to assume that Jerome included Baruch as tacked on to the end of Jeremiah, a common practice in that day.
Equally important is that regardless of Jerome's private opinions, he submitted to the authority of the church, and included the full Deuterocanon (Tobit, Judith, 1 & 2 Maccabees, the Book of Wisdom, etc) in his Latin Vulgate translation, fully counting them as scripture.
Here's Jerome submitting on Judith based on the authority of the Nicene Council, even if he does not personally approve of the book:
Jerome's Preface to Judith
Among the Hebrews the Book of Judith is found among the Hagiographa, the authority of which toward confirming those which have come into contention is judged less appropriate. [...] But because this book is found by the Nicene Council to have been counted among the number of the Sacred Scriptures, I have acquiesced to your request...
Here's Jerome discussing multiple versions of the book of Daniel that were available, and how he submitted in selecting the one used by the churches - even if he did not believe that translation was good.
What sin have I committed in following the judgment of the churches? But when I repeat what the Jews say against the Story of Susanna and the Hymn of the Three Children, and the fables of Bel and the Dragon, which are not contained in the Hebrew Bible, the man who makes this a charge against me proves himself to be a fool and a slanderer; for I explained not what I thought but what they commonly say against us.
Here is Jerome noting that the Jews of his day exclude Tobit from Divine Scriptures - but then submitting to the authority of the church in including it.
Jerome's Preface to Tobit
...the book of Tobias, which the Hebrews exclude from the catalogue of Divine Scriptures, being mindful of those things which they have titled Hagiographa. I have done enough for your desire, yet not by my study. For the studies of the Hebrews rebuke us and find fault with us, to translate this for the ears of Latins contrary to their canon. But it is better to be judging the opinion of the Pharisees to displease and to be subject to the commands of bishops...
Here's Jerome quoting from the Book of Wisdom as Holy Scripture:
Jerome's Letter 51, Sections 6 & 7
For in the book of Wisdom, which is inscribed with his name, Solomon says: "God created man to be immortal, and made him to be an image of His own eternity." [Wisdom 2:23]... Instead of the three proofs from Holy Scripture which you said would satisfy you if I could produce them, behold I have given you seven.
And finally, here's Jerome quoting from Sirach as scripture:
Jerome's Letter 108, Section 21
...for does not the scripture say: "Burden not yourself above your power?" [Sirach 13:2]
Around 393 AD, the Council of Hippo was held which gave the full New Testament list, and gave an Old Testament list including the full Deuterocanon (Tobit, Judith, 1 & 2 Maccabees, the Book of Wisdom, etc) (Canon xxxvi).
Around 397 AD, the Council of Carthage was held which gave the full New Testament list, and gave an Old Testament list including the full Deuterocanon (Tobit, Judith, 1 & 2 Maccabees, the Book of Wisdom, etc) (Source).
Around 400 AD, Tyrannius Rufinus gave an Old Testament canon list which excluded most of the Deuterocanon - except just like Jerome, note that he did not exclude Baruch (Commentary on the Apostles' Creed, sections 37 & 38). It is likely he included Baruch in his list as tacked on the end of Jerome, a common practice at that time - as he quotes earlier in the same work from Baruch as they sayings of a prophet (section 5).
Rufinus did not count the rest of the Deuterocanon as Apocrypha - rather, he counted them among the scriptures (as part of the Word of God), but he called them "Ecclesiastical" rather than "Canonical". He said they should be read in the churches, though not appealed to for the confirmation of doctrine. They were separate from the Apocrypha, which were not scriptures, and should not be read in the churches (section 38).
Also, Rufinus argued that removing the Deuterocanonical parts of the scriptures would not be a "correction of error" - which gives us confirmation that he indeed included the Deuterocanon as scriptures that weren't to be cut out.
Rufinus' Apology Against Jerome, 2.33
In all this abundance of learned men, has there been one who has dared to make havoc of the divine record handed down to the Churches by the Apostles and the deposit of the Holy Spirit? For what can we call it but havoc, when some parts of it are transformed, and this is called the correction of an error? For instance, the whole of the history of Susanna, which gave a lesson of chastity to the churches of God, has by him been cut out, thrown aside and dismissed. The hymn of the three children, which is regularly sung on festivals in the Church of God, he has wholly erased from the place where it stood. But why should I enumerate these cases one by one, when their number cannot be estimated?
Around 419 AD, another Council of Carthage was held which gave the full New Testament list, and gave an Old Testament list including the full Deuterocanon (Tobit, Judith, 1 & 2 Maccabees, the Book of Wisdom, etc) (Canon 24).
During this period of time, for about a thousand years Jerome's Latin Vulgate (which included the Deuterocanon) was the bible of Christianity.
Somewhere between 600-1000 AD, the Jewish Masoretes publish their text + canon. This canon matches the modern Protestant Old Testament canon - though these Jews reject the entire New Testament as authoritative.
Around 1442 AD, the Council of Florence was held which gave the full New Testament list, and gave an Old Testament list including the full Deuterocanon (Tobit, Judith, 1 & 2 Maccabees, the Book of Wisdom, etc) (Session 11-4 February 1442).
Around 1534 AD, Protestant Martin Luther published his Bible translation. In it, he moves Deuterocanon to the end of his Old Testament and labels them "Apocrypha" (Apocrypha introduction, Luther’s Bible). Similar to his Old Testament Apocrypha, he was skeptical of Hebrews, James, Jude and Revelation, and stuck them at the end of his New Testament, saying "Up to this point we have had to do with the true and certain chief books of the New Testament. The four which follow have from ancient times had a different reputation" (Preface to the Epistle to the Hebrews). He also notes that in his judgment, Esther deserves to be excluded from the Old Testament canon more than the rest of the Deuterocanon (Bondage of the Will, Section XLVI).
Even with Luther being against these Old Testament and New Testament books, he didn't remove them from his Bible translation - he just shifted them to the end of each Testament.
Around 1546 AD, the Catholic Council of Trent was held, which again proclaimed the canon including the full Deuterocanon (Tobit, Judith, 1 & 2 Maccabees, the Book of Wisdom, etc) (The Fourth Session, DECREE CONCERNING THE CANONICAL SCRIPTURES).
Around 1547 AD, John Calvin blasted the Council of Trent, including their proclamation of canon. Calvin says that Catholics give full authority to the Deuterocanonical books, which lets them "prove Purgatory", "the worship of saints", and "exorcisms". He identifies the Deuterocanon as "ecclesiastical books, which might indeed be read to the people, but were not entitled to establish doctrine", as he says Ruffinus and Jerome did. He also notes that he is not "I am not one of those, however, who would entirely disapprove the reading of those books" (Acts of the Council of Trent with the Antidote, ON THE FOURTH SESSION).
Note that in Calvin's list of ecclesiastical but not canonical books, he lists the Deuterocanon... but leaves off Baruch. Ruffinus and Jerome (whom Calvin quotes) likewise leave off Baruch. This is intriguing because Calvin quotes from Baruch, calling him a prophet - just like Ruffinus and Jerome. Calvin even goes so far as to say that it is likely Paul, in his letter 1 Corinthians, borrowed from Baruch (Commentary on Corinthians - Volume 1, 1 Corinthians 10:19-24, Section 20). From this evidence, it appears Calvin accepted Baruch as canon as part of Jeremiah.
Around 1572 AD, the Protestant Church of England's Thirty-Nine Articles gave an Old Testament list that put the Deuterocanon not on the same level as the rest of the canonical books - the Deuterocanon was to be read for example of life and instruction of manners, but not used to establish doctrine (Article 6). The Deuterocanon was however still a part of the Holy Scriptures, and was included in the Church of England's King James Bible of 1611.
Around 1642 AD the English Civil War broke out, and it lasted until 1649 AD. The Long Parliament of 1644 decreed that only the Hebrew Canon would be read in the Church of England, and in 1647 the Westminster Confession of Faith was issued which decreed a 39-book Old Testament, with the Deuterocanon excluded completely from the Bible.
With the restoration of the monarchy to Charles II of England (1660-1685), the Church of England was once again governed by the Thirty-Nine Articles, and thus emphatically maintained that the Deuterocanon is part of the Bible and is to be read with respect by her members (but not used to establish any doctrine).
The modern Protestant bible most widely in use by Presbyterians, Baptists, and many other groups is descended from the Church of England's temporary list, propagated during their civil war in the 1640s. Never before then had a Christian used a bible with the exact same books as the modern Protestant list.