There are no sections of the protestant Bible that were taken out, such as the books of the Apocrypha. The New Testament was affirmed in 367 AD (in Athanasius' Easter Letter from Alexandria) with the 27 books we still have in it. The same 27 books were approved by the African Councils of Hippo (393 AD) and Carthage (397). No books were ever taken out. In 1546 at The Council of Trent, after Luther split off from the Catholic Church, the Catholics added in what we call the Apocrypha—in the neighborhood of a dozen books. Some Catholics say that the Council of Trent affirmed those books back in the 4th and 5th century under Augustine, but the truth is that those books were always in dispute, and especially in dispute between Jerome and Augustine. Augustine wanted them in; Jerome said they didn't belong. Jerome's Vulgate, containing the same books we have in our Bibles today (
http://en.wikipedia.org/wiki/Vulgate#Contents), became the official "Scripture" of the Catholic Church through the ensuing centuries. The books of the Apocrypha had been in the Septuagint, and they were occasionally quoted by the church fathers (but never by the apostles). All through the Middle Ages, those books of the Apocrypha were a matter of dispute in the Catholic Church, but they were never officially brought in until 1546 at the Council of Trent, after the Protestants had broken off under Martin Luther.