Thomas Jefferson believed Native American peoples to be a noble race who were "in body and mind equal to the whiteman" and were endowed with an innate moral sense and a marked capacity for reason. Nevertheless, he believed that Native Americans were culturally and technologically inferior.  Like many contemporaries, he believed that Indian lands should be taken over by white people.
Jefferson never removed any Native Americans. However, in private letters he did suggest various ideas for removing tribes from enclaves in the East to their own new lands in lands west of the Mississippi. Indian Removal was passed by Congress in 1831, long after he died. Before and during his presidency, Jefferson discussed the need for respect, brotherhood, and trade with the Native Americans, and he initially believed that forcing them to adopt European-style agriculture and modes of living would allow them to quickly "progress" from "savagery" to "civilization". Beginning in 1803, Jefferson's private letters show increasing support for the idea of removal. Jefferson maintained that Indians had land "to spare" and, he thought, would willingly exchange it for guaranteed supplies of food and equipment.
Jefferson was fascinated with Indian cultures and languages. His home at Monticello was filled with Indian artifacts obtained from the Lewis and Clark expedition. He collected information on the vocabulary and grammar of Indian languages.
Andrew Jackson is often credited with initiating Indian Removal, because Congress passed the Indian Removal Act in 1831, during his presidency, and also because of his personal involvement in the forceful removal of many Eastern Indian tribes. Congress was implementing suggestions laid out by Jefferson in a series of private letters that began in 1804, although Jefferson did not implement the plan during his own presidency. The rise of Napoleon in Europe, and rumor of a possible transfer of the Louisiana Territory from the Spanish empire to the more aggressive French, was cause for consternation amongst some people in the American republic. Jefferson advocated for the militarization of the Western border, along the Mississippi River. He felt that the best way to accomplish this was to flood the area with a large population of white settlements.
Still recovering from the American Revolutionary War, the U.S. federal government was unable to risk starting a broad conflict with the powerful tribes that surrounded their borders. They were worried that this would cause a broader Indian War, in which the Indians would perhaps be joined by Britain, France or Spain. In his instructions to Meriwether Lewis, Jefferson emphasized the necessity for treating all Indian tribes in the most conciliatory manner.
Jefferson wanted to expand his borders into the Indian territories, without causing a full-blown war. Jefferson's original plan was to coerce native peoples to give up their own cultures, religions, and lifestyles in favor of western European culture, Christian religion, and a sedentary agricultural lifestyle. Jefferson's expectation was that by assimilating the natives into a market-based, agricultural society and stripping them of their self-sufficiency, they would become economically heavily dependent on trade with white Americans, and would thereby be willing to give up land that they would otherwise not part with, in exchange for trade goods or to resolve unpaid debts.
In an 1803 private letter to William Henry Harrison, Jefferson wrote:
Jefferson believed that this strategy would "get rid of this pest, without giving offence or umbrage to the Indians". He stated that Harrison was to keep the contents of the letter "sacred" and "kept within [Harrison's] own breast, and especially how improper for the Indians to understand. For their interests and their tranquility, it is best they should see only the present age of their history."
In cases where Native tribes resisted assimilation, Jefferson believed that to avoid war and probable extermination they should be forcefully relocated and sent west. As Jefferson put it in a letter to Alexander von Humboldt in 1813:
He told his Secretary of War, General Henry Dearborn (who was the primary government official responsible for Indian affairs): "if we are constrained to lift the hatchet against any tribe, we will never lay it down until that tribe is exterminated, or driven beyond the Mississippi."
Jefferson's first promotions of Indian Removal were between 1776 and 1779, when he recommended forcing the Cherokee and Shawnee tribes to be driven out of their ancestral homelands to lands west of the Mississippi River. Indian removal, said Jefferson, was the only way to ensure the survival of Native American peoples. His first such act as president, was to make a deal with the state of Georgia that if Georgia were to release its legal claims to discovery in lands to the west, then the U.S. military would help forcefully expel the Cherokee people from Georgia. At the time, the Cherokee had a treaty with the United States government which guaranteed them the right to their lands, which was violated in Jefferson's deal with Georgia.
Main article: Bibliography of Thomas Jefferson
Thomas Jefferson: The Art of Power by Jon Meacham.