Freemasonry has variously been said to be an institutional outgrowth of the medieval guilds of stonemasons, a direct descendant of the "Poor Fellow-Soldiers of Christ and the Temple of Solomon in Jerusalem" (the Knights Templar), an offshoot of the ancient Mystery schools, an administrative arm of the Priory of Sion, the Roman Collegia, the Comacine masters, intellectual descendants of Noah, among other various and sundry origins. Others claim that it dates back only to the late 17th century, and has no real connections at all to earlier organizations.

These theories are noted in numerous different texts, and the following are but examples pulled from a sea of books:

A History of Freemasonry by H.L. Haywood and James E. Craig, pub. circa 1927
The Holy Blood and The Holy Grail by Michael Baigent, Richard Leigh, and Henry Lincoln, pub. 1982
Born in Blood by John Robinson, pub. 1989

Much of the history of Masonry is highly speculative, and the precise origins of Freemasonry may be lost in history. It is thought by many that Freemasonry cannot be a straightforward outgrowth of medieval guilds of stonemasons. Amongst the reasons given for this conclusion, well documented in Born in Blood, are the fact that stonemasons' guilds do not appear to predate reasonable estimates for the time of Freemasonry's origin, that stonemasons lived near their worksite and thus had no need for secret signs to identify themselves, and that the "Ancient Charges" of Freemasonry are nonsensical when thought of as being rules for a stonemasons' guild.

Freemasonry is said by some, especially amongst Masons practicing the York Rite, to have existed even at the time of King Athelstan of England, in the 10th century C.E. Athelstan is said by some to have been converted to Christianity in York, and to have issued the first Charter to the Masonic Lodges there. This story is not currently substantiated (the dynasty had already been Christian for centuries).

Some members of The Church of Jesus Christ of Latter-day Saints note similarities between the church's sacred "Endowments" performed in LDS temples, and Masonic rituals. Some Mormons have said this similarity may be because the Masonic rituals are descended from those given by God at the Temple of Solomon, and still contain many of the original truths. It may also be that early Mormon leaders (including Joseph Smith) were members of Freemasonry and incorporated its liturgy into the new religion.

A more historically reliable (although still not unassailable) source asserting the antiquity of Freemasonry is the Halliwell Manuscript, or Regius Poem, which is believed to date from ca. 1390, and which makes reference to several concepts and phrases similar to those found in Freemasonry. The manuscript itself refers to an earlier document, of which it seems to be an elaboration.
 

It seems reasonable to suppose that, whatever its precise origins, Freemasonry provided a haven for the unorthodox and their sympathizers during a time when such activity could result in one's death, and that this has something to do with the tradition of secret meetings and handshakes. As the Middle Ages gave way to the Modern Age, the need for secrecy subsided, and Freemasons began to openly declare their association with the fraternity, which began to organize itself more formally. In 1717, four Lodges that regularly met at the "Apple-Tree Tavern, the Crown Ale-House near Drury Lane, the Goose and Gridiron in St. Paul's Churchyard, and the Rummer and Grapes Tavern in Westminster" in London, England combined together and formed the first public Grand Lodge, the Grand Lodge of England (GLE). The years following saw Grand Lodges open throughout Europe as the new Freemasonry spread rapidly. How much of this was the spreading of Freemasonry itself, and how much was the public organization of pre-existing secret Lodges, is not possible to say with certainty. The GLE in the beginning did not have the current three degrees, but only the first two (Entered Apprentice and Fellow Craft). The third degree (Master Mason) appeared, so far as we know, around 1725.

The GLE, along with those jurisdictions with which it was in amity, later came to be known colloquially as the Moderns, to distinguish them from a newer, rival group of Freemasonry, known as the Antients. The Antients broke away and formed their own Grand Lodge in 1753, prompted by the GLE's making changes to the secret modes of recognition. Tensions between the two groups were very high at times – the Antients tended to be more working class in membership, and probably more Christian, while the Moderns were more aristocratic and educated, and less religiously orthodox. Benjamin Franklin was a Modern and a Deist, for instance, but by the time he died, his Lodge had gone Antient, and would no longer recognize him as one of their own, declining even to give him a Masonic funeral. It has been speculated that the Antients desired a more Christian style of Masonry, since they made popular a higher degree, called the "Holy Royal Arch", which is generally thought of as having a more Christian flavor than the first three degrees.

This schism was healed in the years following 1813, when the competing Grand Lodges were amalgamated into the United Grand Lodge of England (UGLE), by virtue of a delicately worded compromise which returned the modes of recognition to their pre-1753 form, and kept Freemasonry per se as consisting of three degrees only, but which was ambiguously worded so as to allow the Moderns to think of the Antient Royal Arch degree as an optional higher degree, while still allowing the Antients to view it as the completion of the third degree. This compromise, along with subsequent changes made in 1815, left English Masonry still clearly not Christian, but at the same time somewhat less comfortable for unorthodox members, such as Deists and Pantheists. The merger also marked a leveling of the Masonic membership, in terms of social class and education.

Because both the Antients and the Moderns had daughter Lodges throughout the world, and because many of those Lodges still exist, there is a great deal of variability in the Ritual used today, even between UGLE-recognized jurisdictions. Most Lodges conduct their Work in accordance with an agreed-upon single Rite, such as the York Rite popular in the United States, or the Canadian Rite.

A second great schism in Freemasonry occurred in the years following 1877, when the Grand Lodge of France (GOdF) started accepting atheists unreservedly. While the issue of atheism is probably the greatest single factor in the split with the GOdF, the English also point to the French recognition of women's Masonry and co-Masonry, as well as the tendency of French Masons to be more willing to discuss religion and politics in Lodge. While the French curtail such discussion, they do not ban it as outright as do the English. The schism between the two branches has occasionally been breached for short periods of time, especially during the First World War when American Masons overseas wanted to be able to visit French Lodges.