As he reviewed the reports of the Lewis and Clark expedition, Thomas Jefferson read of encounters with the Oceti Sakowin, Mandan, Shoshone, Nez Perce, and various other Native American communities. Although these Indian Nations were relatively new to Jefferson, Native Americans were not, as Jefferson's personal encounters with them began during his boyhood in Virginia and extended through his public career and into his retirement. Over time and in varying circumstances, he viewed Native Americans as subjects of intellectual curiosity or saw them in political terms as enemies in war or partners in peace. Jefferson's long public career during a formative time period allowed him to shape the relations between the United States and the various Native American Nations during the early years of America and beyond.

Jefferson the Virginian and Native Americans

In his retirement years Jefferson recalled the Native Americans he had encountered as a boy in Virginia, noting especially the Cherokee warrior, Ostenaco (ᎤᏍᏔᎾᏆ, identified as Outassete by Jefferson). But such events would have already been fairly rare in the Virginia of Jefferson's boyhood. By the time of his birth in 1743, the Native American presence in Virginia had been greatly diminished by disease and warfare with white settlers. The Native American Nations remaining inside Virginia were mostly small in size and population during this period. Often categorized by language family, these groups included the Algonkian-speaking nations that were remnants of the once-powerful Powhatan Confederacy, such as the Mattaponi, the Pamunkey, the Chickahominy, the Rappahannock, the Nansemond, and the Patawomeck, the Siouan-speaking nations such as the Monacan, whose homelands encompassed Monticello, the Saponi and Tutelo, and a group of Iroquoian-speakers, including the Meherrin, the Cheroenhaka, Nottoway, and in deep southwest Virginia, the Cherokee, among others. Other tribal groups surely had descendants in Virginia at the time, and people moved frequently as the impacts of ongoing colonization forced change over time. As their populations dwindled, Virginians became less concerned with these Native American communities and more preoccupied with the powerful Native American Nations outside their borders, as settlements of white and Black Virginians now extended to the foot of the Appalachian Mountains.

In 1744, Virginia signed a treaty with the Haudenosaunee (The Six Nations of the Iroquois) that granted land on the west side of the Appalachians to Virginia. The Haudenosaunee claimed to have conquered all of the Tribal Nations of the Ohio Valley, so the Virginians could, in turn, claim land rights to all the Ohio Valley and the area around the Great Lakes. The Indigenous Nations of the Ohio Valley, particularly the Shawnee and the Miami, did not acknowledge such claims and violently resisted the attempts of Virginians to settle in what is today West Virginia, Kentucky, and western Pennsylvania.

In order to reduce the ensuing violence along the frontier, King George III issued a proclamation in 1763 that prohibited any British settlements west of the Appalachians. But as agents employed by the British ministry continued trading with Native Americans in the Ohio Valley Indians, colonists tended to view their conflicts with the Shawnee and Miami Indians coupled with the King's proclamation as a plot to curtail their rights. These issues became embedded in the Declaration of Independence when Jefferson wrote that the King had "endeavored to bring on the inhabitants of our frontiers, the merciless Indian savages, whose warfare is an undistinguished destruction of all ages, sexes, and conditions." Jefferson's description of American Indian warriors as "merciless savages" clearly demonstrates the prejudices common among mid-eighteenth-century white Virginians.

Yet as Governor of Virginia during the Revolutionary War, Jefferson welcomed a delegation from the Kaskaskia. This followed a campaign in the Ohio Valley of Virginia militia led by George Rogers Clark, older brother of William Clark. There, Clark made alliances with some of the Native Nations, including the Kaskaskia of the Illinois country, and then attacked the British and the Indigenous Nations allied with them at villages in present-day Illinois and Indiana. This warfare put Virginia's government into direct contact with western Native Nations and precipitated the visit of the Kaskaskia delegation with Virginia's governor. 

In an exchange of speeches with the leader of the Kaskaskia, a chief of partial French ancestry named Jean Baptiste du Coigne, Jefferson expressed his ambitions for the future of the Anglo-American and Native American relationship. He looked forward to the day when the Indians would adopt white American ways and the two groups would live together in peace. Jefferson's speech prefigured the manner in which he, and most white Americans, would view Native Americans in the decades to come. They worried about Native Americans becoming enemies in times of war, and they sought to keep them at peace through treaties and through a project of "civilization" that would try to make Native American culture resemble that of the Anglo-Americans.