The Canon of Scripture
Protestants, Catholics, and most Orthodox agree now 1 that the New Testament should consist at least of the 27 Books (Matthew through Revelation/Apocalypse) that the Catholic Church determined were canonical, but the Protestant Old Testament is lacking 7 entire books 2 (Tobias, Judith, Wisdom, Ecclesiasticus/Sirach, Baruch, I Maccabees, and II Maccabees), 3 chapters of Daniel and 6 chapters of Esther, leaving them with 66 incomplete books while Catholic Bibles have 73 books. How did this come to be?
Background The canon of the Old Testament that Catholics use is based on the text used by Alexandrian Jews, a version known as the "Septuagint" (also called "LXX" or "The Seventy") and which came into being around 280 B.C. as a translation of then existing texts from Hebrew into Greek by 72 Jewish scribes (the Torah was translated first, around 300 B.C., and the rest of Tanach was translated afterward).
It was a standard Jewish version of the Old Testament, used by the writers of the New Testament, as is evidenced by the fact that Old Testament references found in the New Testament refer to the Septuagint over other versions of the Old Testament. Let me reiterate: the then 300+ year old Septuagint version of Scripture was good enough for Matthew, Mark, Luke, John, and Paul, etc., which is evident in their referencing it over 300 times (out of 350 Old Testament references!) in their New Testament writings -- and the Septuagint includes 7 books and parts of Esther and Daniel that were removed from Protestant Bibles some 1,500 years after the birth of Christ.
The Septuagint is the Old Testament referred to in the Didache or "Doctrine of the Apostles" (first century Christian writings) and by Origen, Irenaeus of Lyons, Hippolytus, Tertullian, Cyprian of Carthage, Justin Martyr, St. Augustine and the vast majority of early Christians who referenced Scripture in their writings. The Epistle of Pope Clement, written in the first century, refers to the Books Ecclesiasticus and Wisdom, analyzed the book of Judith, and quotes sections of the book of Esther that were removed from Protestant Bibles.
Bottom line: the Septuagint was the version of the Old Testament accepted by the very earliest Christians (and, yes, those 7 "extra" books were found among the Dead Sea Scrolls which date between 168 B.C. and A.D. 68, and which by the way, support both the Septuagint and the 6th - 10th c. A.D. Masoretic texts in various ways, but supporting the Septuagint on average. 3 ).
The deuterocanonical books were, though, debated in the early Church, and some Fathers accorded them higher status than others (hence the Catholic term for them: "deuterocanonical," or what St. Cyril of Jerusalem called "secondary rank," as opposed to the other books which are called "protocanonical"). But all the Fathers believed as did St. Athanasius, who, in one of his many Easter letters, names the 22 Books all Christians accept and then describes the deuterocanonicals as "appointed by the Fathers to be read by those who newly join us, and who wish for instruction in the word of godliness." Church Councils listed and affirmed the present Catholic canon, which was only formally closed at the Council of Trent in the 16th century.
So what happened? In the 16th c., Luther, reacting to serious abuses and clerical corruption in the Latin Church, to his own heretical theological vision (see articles on sola scriptura and sola fide), and, frankly, to his own inner demons, removed those books from the canon that lent support to orthodox doctrine, relegating them to an appendix. Removed in this way were books that supported such things as prayers for the dead (Tobit 12:12; 2 Maccabees 12:39-45), Purgatory (Wisdom 3:1-7), intercession of dead saints (2 Maccabees 15:14), and intercession of angels as intermediaries (Tobit 12:12-15). Ultimately, the "Reformers" decided to ignore the canon determined by the Christian Councils of Hippo and Carthage (and reaffirmed and closed at the Council of Trent4), and resort solely to those texts determined to be canonical at the Council of Jamnia.
The Council of Jamnia? Now we have to back up a bit: around A.D. 90-100, after the Temple fell, a rabbinical school was formed by Johanan ben Zakkai. The "Council of Jamnia" (also called "Jabneh" or "Javneh") is the name given to the decisions made by this pharisaic school. I repeat: the gathering at Jamnia was a Jewish, not a Christian, "council" consisting of Pharisees some 40 years after the Resurrection of our Lord. At that time, Jews were being scattered, and the very existence of Jewry per the Pharisees' vision of "Jewry" was being threatened. At this time, too, Christianity was growing and threatening that same Jewish identity, resulting in severe persecution of Christians by Jews. In reaction to these things and to the fact that "Nazarenes" (i.e., "Christians", who at that time were overwhelmingly Hebrew) used the Septuagint to proselytize other Jews, Zakkai convened the Jamnian school with the goals of safeguarding Hillel's Oral Law, deciding the Jewish canon (which had theretofore been, and possibly even afterward remained 5, an open canon!), and preventing the disappearance of Jewry into the Diaspora of the Christian and Roman worlds. So, circling their wagons, they threw out the Septuagint that they had endorsed for almost 400 years. Note that at the time of Christ, most Jews spoke Aramaic, Latin (the official language of the area), and/or Greek (the lingua franca at that time), not Hebrew, which was a sacred language used by priests for the Hebrew liturgy. In any case, a new Greek translation was created by Aquila -- but one without the ancient Septuagint's language that proved more difficult for the Jews to defend against when being evangelized by the Christians, the point being that any idea that a book "had" to have been written in Hebrew to be "Biblical" wasn't the issue.
Moving the story along: in other words, the Protestant "Reformers" decided against the canon held dear by the Apostles in favor of a canon determined by Pharisees some 40 years after Jesus rose from the dead -- the same Pharisees who denied the Truths of the entire New Testament, even accusing the "Nazarenes" of stealing Jesus' body from the tomb and lying to the world! (Interestingly, it was Zakkai's successor, Gamaliel, who forced the "Nazarenes" out of the synagogues. Gamaliel also made it obligatory for Jews to pray the "Prayer of Eighteen Petitions," the 12th petition, which is still prayed today, known as the birkat, being "For apostates may there be no hope, and may the Nazarenes and heretics suddenly perish.")
And do you know why the Book of Maccabees was thrown out by the Jewish Council? Because the Council was conducted under the auspices of the Flavian Roman Emperors and they decided that that particuar book, which tells of the Maccabean Revolt, might be inflammatory and incite rebellion by the Jews. So, all those Protestant Bibles are lacking the Book of Maccabees, which speaks clearly of praying for the dead, because a pagan emperor pressured the Pharisees, around 40 years after the Resurrection of Christ, to exclude it. And lest anyone is still tempted to think that it was the "Roman Church" that came up with these books and that they were not written by pre-Christ Jews (an assertion I've actually read at "Messianic" websites), Jews in other parts of the world who didn't get news of the Council of Jamnia's decisions still use those "extra" 7 books to this very day (research the canon used by Ethiopian Jewry).
Conclusion Me, I will trust the version of the Old Testament that was loved by Peter and Paul.
But there is a bigger lesson in all this confusion over not only the canon but proper translation of the canon (see footnotes), especially considering that even within the Catholic Church there have been differing opinions by individual theologians about the proper place of the deuterocanonicals (not that an individual theologian's opinions count for Magisterial teaching!). The lesson, though, is this: relying on the "Bible alone" is a bad idea; we are not to rely solely on Sacred Scripture to understand Christ's message. While Scripture is "given by inspiration of God, and is profitable for doctrine, for reproof, for correction, for instruction in righteousness" (2 Timothy 3:16-17), it is not sufficient for reproof, correction and instruction in righteousness. It is the Church that is the "pillar and ground of Truth" (1 Timothy 3:15)! Jesus did not come to write a book; He came to redeem us, and He founded a Sacramental Church through His apostles to show us the way. It is to them, to the Church Fathers, to the Sacred Deposit of Faith, to the living Church that is guided by the Holy Spirit, and to Scripture that we must prayerfully look.
1 Luther wanted to remove the Epistle of James, Esther, Hebrews, Jude and Revelation. Calvin and Zwingli also both had problems with the Book of Revelation, the former calling it "unintelligible" and forbidding the pastors in Geneva to interpret it, the latter calling it "unbiblical". The Syrian (Nestorian) Church has only 22 books in the New Testament while the Ethiopian Church has 8 "extra." The first edition of the King James Version of the Bible included the "Apocryphal" (ie, Deuterocanonical) Books.
2 The 7 books removed from Protestant Bibles are known by Catholics as the "Deuterocanonical Books" (as opposed to the "Protocanonical Books" that are not in dispute), and by Protestants as the "Apocrypha."
3 By the way, "Masoretic texts" refers to translations of the Old Testament made by rabbis between the 6th and 10th centuries; the phrase doesn't refer to ancient texts in the Hebrew language. I mention this because, apparently, some people think that the Masoretic texts are the "original texts" and that, simply because they are in Hebrew, they are superior.
In any case, the Latin Church in no way ignored the post-Temple rabbincal texts. Some Old Testament translations of the canon used by the Latin Church were also based in part on rabbinical translations, for example St. Jerome's 5th c. Latin translation of the Bible called the Vulgate.
Some Protestants claim that the "Apocrypha" (i.e., the Deuterocanonical Books) are not quoted in the New Testament so, therefore, they are not canonical. First, this isn't true; see Relevant Scripture below. Second, going by that standard of proof, we'd have to throw out Joshua, Judges, Ruth, 2 Kings, 1 Chronicles, 2 Chronicles, Ezra, Nehemiah, Esther, Ecclesiastes, Song of Solomon, Lamentations, Obadiah, Nahum, and Zephaniah because none of these Old Testament Books are quoted in the New Testament.
4 Many non-Catholic Christians like to accuse Catholics of "adding" Books to the Bible at the 16th c. Council of Trent. This is absolutely, 100% false. This Council, among other things, simply affirmed the ancient accepted books in the face of Protestant tinkering. How could Luther have relegated the deuterocanonical books to an appendix if they hadn't already been accepted in the first place? The Gutenberg Bible was printed in 1454 -- and it included the deuterocanonical Books. How could the Church have "added" them at the Council of Trent that began 91 years later? I defy any Protestant to find a Bible in existence before 1525 that looked like a modern Protestant Bible! Most Protestant Bibles included the deuterocanonical Books until about 1815, when the British and Foreign Bible Society discontinued the practice! And note that Jews in other parts of the world who weren't around to hear the Council of Jamnia's decision in A.D. 100 include to this day those "extra" 7 books in their canon. Do some research on the canon used by Ethiopian Jewry.
5 There is debate as to whether the Council of Jamnia actually "closed" the Jewish canon because debate continued among Jews for hundreds of years afterward as to which books should be included or excluded. Even into the 3rd century A.D., controversy surrounded Ezekiel, Proverbs, Ruth, Esther, and others.
Scripture mentioned in the above article Tobit 12:15
I am Raphael, one of the seven holy angels who present the prayers of the saints and enter into the presence of the glory of the Holy One. [see Revelation 1:4 and 8:3-4 below]
2 Maccabees 7:29
[A mother speaking to her son:] Do not fear this butcher, but prove worthy of your brothers. Accept death, so that in God's mercy I may get you back again with your brothers. [see Hebrews 11:35 below]
2 Maccabees 12:44
For if he were not expecting that those who had fallen would rise again, it would have been superfluous and foolish to pray for the dead. [see 1 Corinthians 15:29 below]
2 Maccabees 15:14
And Onias spoke, saying, "This is a man who loves the brethren and prays much for the people and the holy city, Jeremiah [bodily dead], the prophet of God."
1 Corinthians 15:29
Otherwise, what do people mean by being baptized on behalf of the dead? If the dead are not raised at all, why are people baptized on their behalf? [see 2 Maccabees 12:44 above]
Women received their dead raised to life again: and others were tortured, not accepting deliverance; that they might obtain a better resurrection. [see 2 Maccabees 7:29 above]
...Grace be unto you, and peace, from him which is, and which was, and which is to come; and from the seven Spirits which are before his throne. [see Tobit 12:15 above]
And another angel came and stood at the altar with a golden censer; and he was given much incense to mingle with the prayers of all the saints upon the golden altar before the throne; and the smoke of the incense rose with the prayers of the saints from the hand of the angel before God. [see Tobit 12:15 above]