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Thomas Jefferson's connections to fraternal organizations have often been misunderstood. He is frequently, yet falsely, linked to the Freemasons. Comments that he made in his correspondence suggest that he had a generally negative opinion of fraternal organizations.
Even though standard histories of the Freemasons fail to include Jefferson in their rosters of early members, a persistent popular tradition claims Jefferson for Freemasonry. The tradition may have had its genesis at a ceremony marking the laying of the cornerstone at the University of Virginia. On the morning of October 6, 1817, a large crowd gathered at the site of the first pavilion. According to Philip A. Bruce, “the doors of all the stores were locked, private houses shut up, and the entire population of the little town darkened the road to the College.” In addition to the citizenry of Charlottesville, James Madison, James Monroe, and Jefferson were also present. The cornerstone, Bruce says, was laid "with the customary state by Lodges; Reverend William King was the chaplain, John M. Perry, the architect, and Alexander Garrett, the worthy grand-master. President Monroe applied the square and plumb, the chaplain asked a blessing on the stone, the crowd buzzed, and the band played ‘Hail Columbia.’” Evidently it was customary for Masons to direct many public ceremonies, such as laying cornerstones, opening bridges, and dedicating halls. Thus surrounded by Masonic pomp and circumstance, Jefferson must have seemed a part of the organization simply through association. It should be added that Local Lodges 60 and 90 have never claimed Jefferson as a member, either in a regular or honorary capacity.
Another Jeffersonian link to Freemasonry predates the laying of the cornerstone. In 1801, the “Jefferson Lodge” was organized in Surry, Virginia. The name probably reflected republican exuberance after the election of 1800 and should not be taken as evidence for Jefferson’s membership. It is curious, however, to find a lodge named for a non-Mason; the usual practice is to name the lodge after a fellow Mason of local or national stature. The Alexandria Lodge, for example, became Alexandria Washington Lodge after the death of its famous master. Indeed, to name a lodge after an individual is uncommon; most lodges simply assume the name of the town or county where they are located.
Finally, Jefferson's longstanding interest in architecture and mathematics, both prominent in Masonic lore, could have made a Masonic connection likely in the public mind.
However, the fact remains that no references to Masonic membership have been found in Jefferson’s papers, and given his clear aversion to secret societies (Cincinnati, for example), his membership remains unlikely. Masonic scholars have also reached the same conclusion; an especially thorough review of the evidence (or lack thereof) of Jefferson's ties to the Freemasons appears in William Denslow's 10,000 Famous Freemasons. An even more thorough account of failed attempts to confirm Jefferson's rumored Masonic activities in Paris appears in The Encyclopedia of Freemasonry.
Although Jefferson did not belong to the Freemasons, he did claim membership in another secret society – the F.H.C (also known as the Flat Hat Club). The letters F.H.C. are known to stand for Latin words – though the exact words are not known. So instead, the organization has been dubbed the Flat Hat Club. The Flat Hat Club was established in the 1750s at the College of William and Mary and was the first college fraternity in America. It reached a height of activity in the 1770s and lapsed during the Revolutionary War Years. The organization was never revived and no additional branches were established at other colleges, so little information about its activities remains. Thomas Jefferson was a member of the F.H.C. while attending William and Mary in the 1760s.  Jefferson confirmed his membership in the club in a letter to Thomas McAuley dated June 14, 1819, although he also stated that he believed the institution to have “no useful object."
Jefferson’s general feelings towards fraternal organizations are fairly clear in comments he made to George Washington in a letter dated April 16, 1784 in reference to the Society of the Cincinnati. The Society of the Cincinnati was formed on May 13, 1783 by a gathering of officers from the Continental Army. They called their constitution the “Institution,” and this document dictated that membership would pass to the eldest male descendents of founders and allowed for the admission of honorary members. Branches of the organization were established in all thirteen original colonies and France. The stated intention of the society was “perpetuating wartime friendships, aiding the unfortunate and preserving ‘union and national honor’ among the states". Public criticism was strong immediately following the foundation of the society. Many citizens were concerned about the hereditary and honorary membership aspects. They believed that the society was established to lift its members to the position of nobility in a supposedly democratic society and to ensure the financial obligations of Congress towards veterans of the Revolutionary War. George Washington wrote to Thomas Jefferson requesting his opinion of the Society of Cincinnati, because they had recently chosen him for President pro tem.  Jefferson responded to Washington’s letter, listing the concerns of many citizens about the society. He also expressed his own concern that one of the stated purposes of the society – which was to maintain the sense of brotherhood between old comrades in war – would not be fulfilled, because providing a forum for debate between the old comrades would only foster arguments and ruin friendships. Jefferson advised that Washington propose some serious alterations to the society’s constitution (which he admitted would bring the society close to annihilation).These changes included parting “with it’s inheritability, it’s organization and it’s assemblies." Washington obviously took Jefferson’s advice into consideration, as he did submit several suggested changes to the Society’s constitution. These changes included abolishing the hereditary function of the society, striking out any clause with a political tendency, rejecting donations from foreign sources, and restricting the business of the meetings to the election of officers and the disposal of charitable funds. These proposed changes were published in several newspapers. This turned out to be enough to allay the public’s fears about the society, but in reality the changes were not ratified by all of the branches. Whether or not it was earned, public opinion shifted more positively towards the Society in the late 1780s and 1790s and after 1800, the Society became much less active. In fact, most branches had ceased to function by the first quarter of the century. 
Primary Source References
1784 April 16. (Jefferson to George Washington). "I received your favor of the 8th. inst. by Colo. Harrison. The subject of it is interesting, and, so far as you have stood connected with it, has been matter of anxiety to me: because whatever may be the ultimate fate of the institution of the Cincinnati, as in it’s course it draws to it some degree of disapprobation, I have wished to see you stand on ground separated from it; and that the character which will be handed to future ages at the head of our revolution may in no instance be compromitted in subordinate altercations. The subject has been at the point of my pen in every letter I have written to you; but has been still restrained by a reflection that you had among your friends more able counsellors, and in yourself one abler than them all. Your letter has now rendered a duty what was before a desire, and I cannot better merit your confidence than by a full and free communication of facts and sentiments as far as they have come within my observation." 
1800 January 31. (Jefferson to Bishop James Madison). "[Wishaupt] believes the Freemasons were originally possessed of the true principles & object of Christianity, and have still preserved some of them by tradition, but much disfigured. the means he proposes to effect this improvement of human nature are ‘to enlighten men, to correct their morals & inspire them with benevolence. secure of our success, sais he, we abstain from violent commotions. to have foreseen the happiness of posterity & to have prepared it by irreproacheable means, suffices for our felicity. this tranquility of our consciences is not troubled by the reproach of aiming at the ruin or overthrow of states or thrones.’ as Wishaupt lived under the tyranny of a despot & priests, he knew that caution was necessary even in spreading information, and the principles of pure morality. he proposed therefore to lead the Freemasons to adopt this object, and to make the objects of their institution, the diffusion of science & virtue. he proposed to initiate new members into this body by gradations proportioned to his fears of the thunderbolts of tyranny. this has given an air of mystery to his views, was the foundation of his banishment & the subversion of the Masonic order, and is the colour for the ravings against him of Robinson, Barruel & Morse, whose real fears are that the craft would be endangered by the spreading of information reason & natural morality among men."
1817 August 31. (Jefferson to Martha Jefferson Randolph). "Ellen tells me that a request is communicated thro’ Mr Randolph & yourself from the Freemason societies of Charlottesville to be permitted to lay the first brick of the Central college. I do not know that I have authority to say either yea or nay to this proposition, but as far as I may be authorised, I consent to it freely."
1819 June 14. (Jefferson to Thomas McAuley). "I have heard of the Alpha, Phi, Beta and Kappa society, but never understood either it's location or object. when I was a student of Wm, & Mary college of this state there existed a society called the F.H.C. society, confined to a number of six students only, of which I was a member, but it had no useful object. nor do I know whether it now exists." 
- Beha, Ernest. A Comprehensive Dictionary of Freemasonry. New York: Citadel, 1963.
- Beless, James W. "Thomas Jefferson, Freeman." Scottish Rite Journal 3 (1998). Text available online.
- Whalen, William J. Handbook of Secret Organizations. Milwaukee: Bruce, 1966.
- 1. Philip A. Bruce, History of the University of Virginia, 1819-1919 (New York: Macmillan, 1920), 1:189-190.
- 2. Henry Leonard Stillson, History of the Ancient and Honorable Fraternity of Free and Accepted Masons (Boston: Fraternity Publishing Co., 1892), 548.
- 3. William R. Denslow, 10,000 Famous Freemasons from A to J (Kessinger, 2004), Part 1, 1:292. Text available online.
- 4. Albert G. Mackey and H. L. Haywood, The Encyclopedia of Freemasonry (Kessinger, 2003), 2:644-5. Text available online.
- 5. Ibid., 3:11. Text available online.
- 6. Jane Carson, James Innes and His Brothers of the F.H.C. (Williamsburg, Virginia: Colonial Williamsburg, 1965), 2.
- 7. Jefferson to Thomas McAuley, June 14, 1819, in George P. Coleman, The Flat Hat Club and the Phi Beta Kappa Society: Some New Light on Their History (Richmond, VA: Press of the Dietz Printing Co., 1916).
- 8. George Washington to Jefferson, Mount Vernon, April 8, 1784, in PTJ 7:88; recipient's copy available online from the Library of Congress.
- 9. Jefferson to George Washington, Annapolis, April 16, 1784, in PTJ 7:105; letterpress copy available online from the Library of Congress
- 10. Wallace Evan Davies, "The Society of the Cincinnati in New England 1783-1800," WMQ 5, no. 1 (1948): 3-25.
- 11. PTJ, 7:105.
- 12. Founder of the Order of the Illuminati.
- 13. PTJ, 31:350-1.
- 14. Family Letters, 418-19.
- 15. Coleman, The Flat Hat Club, unnumbered page.