From Thomas Jefferson Encyclopedia
"And with regard to English conveniences, they are also an unknown luxury in the United States, where there are only 'little houses' five hundred paces from the house whenever possible. That is very disagreeable in winter with the snow, and in summer when summer complaint, diarrhea, is quite a common ailment. Irénée has done an extraordinary thing for me with a 'little house' twenty-five paces away in a little thicket; and when it rains I should like it better even closer. In Washington, Madam Barlow placed hers at the end of the piazza; that is a great improvement. But that lady has French manners. At Monticello, Mr. Jefferson's home, one has the choice of three hundred paces in the garden and on the terraces or through an underground tunnel, level with the cellars and built for that purpose." -- Pierre S. du Pont de Nemours to his wife, Sept. 28, 1816 
Du Pont de Nemours' remarks reveal that as late as 1816 indoor toilets, with or without flushing mechanisms, were uncommon in America. Such was not the case in Europe. Thomas Jefferson himself had enjoyed the luxury of flush toilets in the Paris townhouse he rented 30 years earlier. But according to du Pont de Nemours, Mrs. Joel Barlow and Thomas Jefferson were among the very few to practice "French manners" on this side of the Atlantic.
Yet his account of the privies at Monticello - the only contemporary one that has come to light — does more to confuse than to settle the question of the location of these conveniences. This could be explained by the fact that more than nine months had elapsed between his December 1815 visit to Monticello and the letter to his wife. Furthermore, owing to delays and miscommunication, the visit occurred while Jefferson was at his retreat, Poplar Forest. And although he confessed to being "overwhelmed by the kindness of Mrs. Randolph" during his three or more days at Monticello, du Pont de Nemours apparently did not experience, let alone see, the "conveniences" that Jefferson had inside the house.
We know from what physical evidence remains that there were three privies in the house proper. In his building notebook, Jefferson referred to these conveniences as "air closets." Two were located off the first- and second-floor south stair passages and a third adjoined Jefferson's bedroom. These interior spaces were shafts lighted by skylights and not much larger than what was needed for a seat. Each shaft extended below the floor to the sub-cellar level, where each joined a single masonry-lined "sink" (also called by Jefferson a "conduit") approximately 2 1/2 feet wide and 3 3/4 feet high with a fall (according to his specifications) of 3 inches in 10 feet. The termination of this tunnel can be seen today about 125 feet east of the house.
The only document that has come to light regarding the construction of these privies is Jefferson's letter of April 24, 1802 informing James Oldham, "I would much rather have the 2d. and 3d. air-closets finished before any thing else, because it will be very disagreeable working in them after even one of them begins to be in use." Since Oldham was a joiner, it is assumed that he was responsible for the finished woodwork in those spaces. But just how the interior privies worked is still a question. Clearly Jefferson's reference to a "sink" implies some transport of waste. An undated plan, roughly sketched by him, shows how water from the higher mountain adjoining Monticello to the south could be piped to both a fish pond near the house and to what appears to be a privy in what is now the alcove of the South Square Room or (assuming another possible interpretation of that part of the plan) the cellar space directly below the Square Room. There is also a line that branches off to the South Piazza—Jefferson's greenhouse.
Nonetheless, all evidence points to mere intent, for nothing has come to light that indicates that a flushing mechanism was in operation or even installed. Nor is there physical evidence to support the intriguing statement from a 1902 publication claiming, "This cellar is said to have had tunnels from it to convey the sewerage out to pits, by earth cars." When the Foundation acquired Monticello in 1923 apparently nothing remained of the Jefferson-period fixtures, and the conversion of the privy shafts into supply and return air ducts for the modern heating and air-conditioning system in 1954 no doubt erased additional evidence. Furthermore, photographs of the tunnel from that time show an earthen floor and not the "slatestone" specified about 1800 for "the sink, and for the covered way, kitchen, & offices."
One hypothesis is that the waste was collected in a pot under each seat and then lowered to the cellar level where it could be removed by opening a door in the passage wall. Although today there are openings in the cellar wall for each of the three shafts at a convenient height, the only door that existed before 1954 is for the privy off the first-floor passage. The other two openings were added, according to the restoration architect Milton Grigg, to provide access to the modern ductwork. And given that the partition walls between all three shafts extend as far down as the cellar floor, there is no way one door could serve the adjoining privies. Another hypothesis is that Jefferson adopted a simple routine of having a slave enter the room and remove the chamber pot from under the seat. As for the "sink," it may have functioned as an air tunnel, supplying the shafts with fresh air drawn by a powerful draft through a connecting chimney flue. Of the three interior privies, only the one adjoining Jefferson's chamber was "restored." In 1955 a wooden seat, typical of the period, was installed.
Two additional conveniences were located at the north and south ends of the passageway that connects the cellars to the stable and kitchen wings. At the North Privy a pit under the seat connects to a straight tunnel that opens in the hillside. It is about 44 feet long and has a descent of 4 ½ inches. Although the South Privy has not been excavated we know that it too was to be served by a tunnel. And although all physical evidence of a mechanism, if any, is gone, the idea of an "earth car," perhaps operated by a pulley system, seems more likely at these two locations. Even so, we know that Jefferson was paying slaves for regularly "cleansing sewers." These payments, which were recorded in his memorandum books sometimes as often as once a month, were usually in the amount of one dollar. The task, however, was never described and so we are at a loss to know if it involved digging out a pit, emptying an "earth car," or some other operation.
It is regrettable that the Jefferson-period fixtures had been removed from the North Privy by the time of the restoration of the northwest dependencies in 1938. We judge from what was recorded as existing, and from what was restored in that year, that all that remains today from Jefferson's period are the stone walls (up to about the top of the window), the window frame, some evidence of plaster (with most of what is left dating from the later nineteenth century), and evidence of early (Jefferson period?) slate paving in the outer passage.
The present floors and plaster walls (with remains of earlier plaster preserved-some with graffiti from the 1850s) date from 1999-2000 as does the single-hole seat, which is based on a Jefferson floor plan and on details of an original seat at Poplar Forest. The stepped-pyramidal roof (based on Jefferson's design) and the inner and outer doors and door frames all date from the partial restoration in 1938. On the matter of doors, Jefferson wrote to James Oldham on June 22,1802, "I think the outer door of the South East necessary must be a panelled door, hung flush with the inside of the wall, and the upper panel (instead of being glass as I before proposed) had better be of Venetian blinds, as that will give air as well as light. As soon as you have done the S.E. necessary, I would rather you would proceed with the N.W. one."
The only other known privy on the mountaintop was located southeast of the house along Mulberry Row. Its location near the nailery is noted on Jefferson's insurance plat from 1796, where it is described as "a necessary house of wood 8. feet square." This might be the one identified by du Pont de Nemours as "three hundred paces in the garden and on the terraces."
It is assumed that the Mulberry Row necessary was for the use of those living and working along that plantation street. More of a question is the use of the two privies off the south stair halls and the ones at the ends of the cellar passageway. We do know that the second-floor privy had what appears to be a cupboard lock operable by a key from the outside, and that the first-floor air-closet had, over a period of time, three or even as many as four different locks. As for the cellar passageway privies, the records tell us that Jefferson wanted one "japanned" closet lock installed on the door to the "North necessary." Other than these few references there is nothing to enlighten us whether all were welcomed or whether use was restricted by gender or status.