For the first two months covered by this volume, Thomas Jefferson is residing at Monticello, avoiding the "rather sickly" season in the nation's capital. His mountaintop house finally has a roof and both daughters and their families come to stay with him. Using cowpox vaccine received from Benjamin Waterhouse, he undertakes what he calls "my experiment," the systematic inoculation of family members and slaves against the smallpox. In Washington, the construction of buildings for the nation's capital moves forward. The walls of the chamber of the House of Representatives now extend "up to the window heads," with only three feet more to go. Jefferson considers the erection of this chamber as well as completion of a "good gravel road" along Rock Creek as crucial for "ensuring the destinies of the city." The interior decoration of the President's House also progresses, with draperies, girandoles, and a chandelier furnishing the circular room. His carriage is ready to be shipped from Philadelphia. As the city takes shape, so too do the operating principles of Jefferson's administration. He dispatches a letter to his heads of department outlining "the mode & degrees of communication" for conducting their business. In mid-November, he enters a period of intense activity in the preparation of his first annual message to Congress, soliciting suggestions but personally drafting the document that he will submit in writing in early December.

The period covered by this volume brings to a conclusion Thomas Jefferson's first year as president. On 8 December he communicates his first annual message to Congress: peace between France and England is restored; a rise in population will increase revenue and help abolish internal taxes; the standing army can be done away with; "peace & friendship" prevail with Indian neighbors. He recommends two particular matters to the attention of Congress: a revision of the laws on naturalization and a review of the Judiciary Act. Two delegations of Indian nations hold conferences with Jefferson and Secretary of War Henry Dearborn in Washington. Jefferson observes that it is good for them to "renew the chain of affection." The president receives a "Mammoth Cheese" as a token of esteem from the citizens of Cheshire, Massachusetts, and the letter from the Danbury Baptists arrives. In his famous reply to the Baptists, Jefferson states that "religion is a matter which lies solely between man & his god." Shortly after legislators arrive in town for the opening of Congress, he begins to entertain at the President's House. He uses such occasions to bridge the divide between the executive and legislative branches and foster political understanding between Republicans and Federalists. As he moves into his second year as president, he is optimistic about his legislative program and the Republican majority in Congress.

Confessing that he may be acting "with more boldness than wisdom," Jefferson in November 1803 drafts a bill to create Orleans Territory, which he entrusts to John Breckinridge for introduction in the Senate. The administration sends stock certificates to France in payment for Louisiana. Relieved that affairs in the Mediterranean have improved with the evaporation of a threat of war with Morocco, the president does not know yet that Tripoli has captured the frigate Philadelphia with its officers and crew. He deals with never-ending issues of appointment to office and quarreling in his own party, while hearing that some Federalists are "as Bitter as wormwood." He shares seeds of the Venus flytrap with Elizabeth Leathes Merry, the British minister's wife. She and her husband, however, create a diplomatic storm over seating arrangements at dinner parties. Having reached St. Louis, Meriwether Lewis reports on the progress of the western expedition. Congress passes the Twelfth Amendment, which will provide for the separate election of president and vice president. In detailed notes made after Aaron Burr calls on him in January, Jefferson records his long-standing distrust of the New Yorker. Less than a month later, a congressional caucus nominates Jefferson for a second term, with George Clinton to replace Burr as vice president. Jefferson makes his first trials of the "double penned writing box" called the polygraph.

Volume 38 opens on 1 July 1802, when Jefferson is in Washington, and closes on 12 November, when he is again there. For the last week of July and all of August and September, he resides at Monticello. Frequent correspondence with his heads of department and two visits with Secretary of State James Madison, however, keep the president abreast of matters of state. Upon learning in August of the declaration of war by Mawlay Sulayman, the sultan of Morocco, much of the president's and the cabinet's attention is focused on that issue, as they struggle to balance American diplomatic efforts with reliance on the country's naval power in the Mediterranean. Jefferson terms the sultan's actions "palpably against reason." In September, he addresses the concerns of the mayor of New York City and the governor of South Carolina that free blacks expelled from Guadeloupe by the French will be landed onto American shores. Although he believes the matter will be dealt with by the states, he also instructs Secretary of the Treasury Albert Gallatin to direct custom house officers to be watchful. In late August, Jefferson is alerted that he has been touched by the "breath of Slander," when James T. Callender's accusations appear in the Richmond Recorder and make public his relationship with Sally Hemings. The president offers no comment, and a month later returns to Washington, where he continues planning for an impending visit by his daughters. Some images inside the book are unavailable due to digital copyright restrictions.

This volume opens on 4 March 1802, the first anniversary of Thomas Jefferson's inauguration as the nation's third president, and closes on 30 June. In March, a delegation of Seneca Indians comes to Washington to discuss their tribe's concerns, and Jefferson names a commissioner to handle a land sale by Oneida Indians to the state of New York. In April, the Senate ratifies a treaty with the Choctaw nation for a wagon road across their lands. Jefferson worries about an increasingly dictatorial France taking back control of New Orleans, prompting him to the intemperate remark that he would "marry" America's fortunes to the British fleet. Charles Willson Peale sends him sketches of the skull of a prehistoric bison found in Kentucky. During the closing, and very frustrating, weeks of Congress, he distracts himself with a cipher devised by Robert Patterson. He prepares lists of books to be purchased for the recently established Library of Congress and also obtains many titles for his own collection. Even while he is in Washington occupied with matters of state, Jefferson has been keeping close watch on the renovations at Monticello. In May, he has Antonio Giannini plant several varieties of grapes in the southwest vineyard, and he orders groceries, molasses, dry Lisbon wine, and cider to be shipped to Monticello in time for his arrival. He looks forward "with impatience" to the moment he can embrace his family once more.

The Louisiana Purchase dominates the months covered in this volume. Jefferson departs for Monticello to enjoy a needed respite after the busy three and a half months he has just spent in the nation's capital. Shortly before leaving Washington, he has a last meeting with his cabinet, after which he issues a proclamation to reconvene Congress on 17 October, three weeks early. It is the "great and weighty" business of the French government’s stunning offer to transfer all of the Louisiana Territory to the United States that necessitates this important gathering. The event brings Jefferson enthusiastic congratulations from his friends and fellow Republicans. With Jefferson’s great success, however, comes the reality of getting the agreement with France approved and implemented. The boundaries of the territory ceded are not even clear. In private letters to his trusted advisers, Jefferson discusses the proper course of action. Should both houses of Congress be called to consider the French offer? Is it prudent to make the substance of a treaty public? And perhaps most vexing, does this executive action require an amendment to the Constitution? Some Federalists criticize the plan, but an expansion of the nation’s territory, proponents argue, will raise America’s stature in the eyes of the world. With the widening of the country’s borders, Jefferson’s project to send an exploratory party westward seems even timelier. William Clark accepts Meriwether Lewis’s invitation to join the expedition, and on the last day of August Lewis begins his journey down the Ohio River, the building of his boat finally complete.

"The Papers of Thomas Jefferson is a projected 60-volume series containing not only the 18,000 letters written by Jefferson but also, in full or in summary, the more than 25,000 letters written to him. Including documents of historical significance as well as private notes not closely examined until their publication in the Papers, this series is an unmatched source of scholarship on the nation's third president."--Publisher description.

This volume opens on 13 November 1802, when Jefferson is in Washington, and closes on 3 March 1803, the final day of his second year as president. The central issue of these months is the closing of the right of deposit at New Orleans, an act that threatens the economic wellbeing of Westerners. Jefferson asks his old friend Pierre Samuel du Pont de Nemours to remind the French government of the strong friendship between the two nations. To disarm the political opposition, the president sends James Monroe, who is respected by the Federalists, to Europe as a special envoy to work with Robert Livingston in negotiating the dispute with France. Jefferson proposes a "bargain" that will result in the acquisition of the Louisiana Territory. In a confidential message to Congress, Jefferson seeks $2,500 to send a small party of men to explore the Missouri River. Congress concurs, and Jefferson's secretary Meriwether Lewis will lead the expedition. Settling the boundaries with Native American lands is a major theme of the volume. In reality, "settling" results in major cessions of Indian lands to the American government. During the months of this volume Jefferson never leaves the capital, even for a brief sojourn at Monticello. He does, however, enjoy a visit of six weeks from his daughters and two of his grandchildren. They participate in Washington society, capture the affection of Margaret Bayard Smith, and brighten Jefferson's days.

Noted historian Barton sets the record straight on the lies and misunderstandings that have tarnished the legacy of Thomas Jefferson.

A definitive scholarly edition of the correspondence and papers of Thomas Jefferson Jefferson continues his pattern of returning home to Monticello for the summer months. He makes a brief visit to Poplar Forest in Bedford County to plan the development of that property. James Hubbard, a young enslaved worker at Monticello, escapes but is captured in Fairfax County. Another slave who has fled, James Hemings, rejects efforts to persuade him to return and disappears. Receiving news of the end of the conflict with Tripoli, Jefferson states that although it is “a small war in fact, it is big in principle.” He devotes much of his attention to relations with Spain. He considers alliance with Great Britain to force a resolution with Spain, then chooses instead to negotiate with France for the purchase of Florida and settlement of matters in dispute with Spain. He drafts bills to organize the militia by age and create a naval militia. Specimens sent by Lewis and Clark arrive. Jefferson calculates that the United States has recently acquired cessions of well over 9 million acres of land from Native Americans. He meets with visiting Creek leaders. Answering a query, Jefferson states that Patrick Henry was “the greatest orator that ever lived” but “avaritious & rotten hearted.”