By Rebecca Morelle
Science reporter, BBC News
Works by mathematician Archimedes and the politician Hyperides had already been found buried within the book, known as the Archimedes Palimpsest.
But now advanced imaging technology has revealed a third text - a commentary on the philosopher Aristotle.
Project director William Noel called it a "sensational find".
The prayer book was written in the 13th Century by a scribe called John Myronas.
But instead of using fresh parchment for his work, he employed pages from five existing books.
Dr Noel, curator of manuscripts at the US-based Walters Art Museum and a co-author of a forthcoming book on the Archimedes Palimpsest, said: "It's a rather brutal process, but it means you can reuse parchment if you are short of it.
"You take books off shelves, you scrub off the text, you cut them up and you make a new book."
In 1906 it came to light that one of the books recycled to form the medieval manuscript contained a unique work by Archimedes.
And in 2002, modern imaging technology not only provided a clearer view of this famous mathematician's words, but it also revealed another text - the only known manuscript of Hyperides, an Athenian politician from the 4th Century BC.
"At this point you start thinking striking one palimpsest is gold, and striking two is utterly astonishing. But then something even more extraordinary happened," Dr Noel told the BBC News website.
One of the recycled books was proving extremely difficult to read, explained Roger Easton, a professor of imaging science at Rochester Institute of Technology, US.
"We were using a technique called multispectral imaging," he said.
This digital imaging technique uses photographs taken at different wavelengths to enhance particular characteristics of the imaged area.
Subtle adjustments of this method, explained Professor Easton, suddenly enabled these hidden words to be revealed.
"Even though I couldn't read Ancient Greek, just the fact that I could see the words gave me shivers," he said.
Foundations of logic
An international team of experts began to scrutinize the ancient words, explained Reviel Netz, professor of ancient science at Stanford University, US and another co-author of the palimpsest book.
A series of clues, such as spotting a key name in the margin, led the team to its conclusion.
"The philosophical passage in the Archimedes Palimpsest is now definitely identified as a relatively early commentary to Aristotle's Categories," said Professor Netz.
He said that Aristotle's Categories had served as the foundation for the study of logic throughout western history.
Further study has revealed the most likely author of this unique commentary is Alexander of Aphrodisias, Professor Robert Sharples from the University College London told BBC News.
If this is the case, he said, "it gives us part of a commentary previously supposed lost by the most important of those ancient commentators on Aristotle".
A provisional translation of the commentary is currently being undertaken.
It reveals a debate on some aspects of Aristotle's theory of classification, such as: if the term "footed" is used for animals, can it be used to classify anything else, such as a bed?
The passage reads:
For as "foot" is ambiguous when applied to an animal and to a bed, so are "with feet" and "without feet". So by "in species" here [Aristotle] is saying "in formula".
For if it ever happens that the same name indicates the differentiae of genera that are different and not subordinate one to the other, they are at any rate not the same in formula.
Dr Noel said: "There is no more important philosopher in the world than Aristotle. To have early views in the 2nd and 3rd Century AD of Aristotle's Categories is just fantastic."
"We have one book that contains three texts from the ancient world that are absolutely central to our understanding of mathematics, politics and now philosophy," he said.
"I am at a loss for words at what this book has turned out to be. To make these discoveries in the 21st Century is frankly nutty - it is just so exciting."There will be a live webcast of Dr Noel and Professor Easton presentation of this latest discovery at the Annual General Meeting of the American Philosophical Society on 1415 BST (0915 EDT) on Thursday 26 April.