Thomas Jefferson's tenure as the third president of the United States began on March 4, 1801, and ended on March 4, 1809. Jefferson assumed the office after defeating incumbent president John Adams in the 1800 presidential election. The election was a political realignment in which the Democratic-Republican Party swept the Federalist Party out of power, ushering in a generation of Jeffersonian dominance in American politics. After serving two terms, Jefferson was succeeded by Secretary of State James Madison, also of the Democratic-Republican Party.

Jefferson took office determined to roll back the Federalist program of the 1790s. His administration reduced taxes, government spending, and the national debt, as well as repealed the Alien and Sedition Acts. He also signed the Military Peace Establishment Act, and adopted an assimilation policy toward Native Americans known as his "civilization program." In 1804, Jefferson appointed William Johnson to the Supreme Court—the first Jeffersonian Republican to serve on the court. In foreign affairs, the major developments were the acquisition of the gigantic Louisiana Purchase from France in 1803, an embargo against trade with both Great Britain and France, and worsening relations with Britain as the United States tried to remain neutral in the midst of the Napoleonic Wars that engulfed Europe. He established a national military academy, used the U.S. Navy to protect merchant ships from Barbary pirates in North Africa, known as the Barbary Wars, and developed a plan to protect U.S. ports from foreign invasion by the use of small gunboats (a plan that proved useless when war came in 1812). He also authorized the Lewis and Clark Expedition to explore the Louisiana Territory and the Pacific Northwest.

During his second term, Jefferson's attention was focused on the trial of then former Vice President Aaron Burr for treason, which resulted in an acquittal, and on the issue of slavery, specifically the importation of slaves from abroad. In 1806, he denounced the international slave trade as a "violation of human rights" and called upon Congress to criminalize it. Congress responded by approving the Act Prohibiting Importation of Slaves the following year. Jefferson appointed Henry Brockholst Livingston and Thomas Todd to the Supreme Court in 1806 and 1807, respectively. The final years of Jefferson's second term were dominated by rising tensions between the United States and Britain, as the Royal Navy began impressing sailors from American ships and attacking American shipping. Jefferson rejected war and instead used economic threats and embargoes that ultimately hurt the U.S. more than Britain. The disputes with Britain continued after Jefferson left office, eventually leading to the War of 1812.

Despite the economic and political troubles caused by naval tensions with Britain, Jefferson was succeeded by his preferred successor in the form of James Madison. His presidency remained highly influential until the American Civil War, but his legacy has shifted and changed overtime, especially regarding his views on slavery. Nonetheless, historical rankings consistently place Jefferson among the nation's most esteemed presidents, and he has been extensively memorialized as an icon of American culture and American republicanism.

Election of 1800

Jefferson ran for president in the 1796 election as a Democratic-Republican, but finished second in the electoral vote to Federalist John Adams; under the laws then in place, Jefferson's second-place finish made him the Vice President of the United States.Wood, 2009, pp. 211–212. Jefferson strongly opposed the Federalist program, including the Alien and Sedition Acts, and the nation became increasingly polarized.Wood, 2009, pp. 267–268. Jefferson and Adams were once again the major presidential candidates of their respective parties in the 1800 presidential election, and Aaron Burr was the Democratic-Republican Party's vice presidential nominee.Wood, 2009, pp. 277–278. Adams's campaign was weakened by unpopular taxes and vicious Federalist infighting over his actions in the Quasi-War.Bernstein, 2003, pp. 126–28; McCullough, 2001, p. 556. The Democratic-Republicans accused the Federalists of being secret monarchists, while the Federalists charged that Jefferson was a godless libertine in thrall to the French.McCullough, 2001, pp. 543–44.

Under the election system in place at the time, the members of the Electoral College were permitted to vote for two names for president; any tie would be decided in a contingent election in the United States House of Representatives. Jefferson and Burr each received 73 electoral votes, while Adams finished in third place with 65 votes. The House of Representatives, still controlled by the Federalists, held a contingent election in February 1801 to decide whether Jefferson or Burr would accede to the presidency. Though some Federalists preferred Burr, Federalist leader Alexander Hamilton strongly preferred Jefferson. On the thirty-sixth ballot of the contingent election, enough Federalist congressmen abstained from the vote to allow Jefferson to win the presidency.Wood, 2009, pp. 278–279, 283–285. Jefferson regarded his victory as "America's Second Revolution," and he hoped to transform the country by limiting government and weakening the power of elites.Appleby, 2003, pp. 4–5

Transition

Before Jefferson could take office, there was a transition period in which he was the president-elect following his victory in the contingent election. The transition between Adams and Jefferson represented the first transfer of the presidency between two different political parties in United States history, and set the precedent for all subsequent inter-party transitions. It was the first time in United States history that a president handed over the presidency to a political opponent.

Unlike modern-day presidential transitions, the transitions at this time were informal affairs, with relatively minimal activity required of the president-elect.

During the transition, Jefferson picked members of his Cabinet. He also selected individuals for less principal positions of his administration, such as Meriwether Lewis to serve as his personal secretary.

Before leaving office, the lame duck Adams, to the outrage of the Democratic-Republicans, at the last minute appointed many federal judges (mostly belonging to the Federalist Party) to fill positions created by the Judiciary Act of 1801. These would be dubbed "midnight judges".Wood, 2009, pp. 419–420. Jefferson denounced this action.

Inauguration

Jefferson's first inauguration, on March 4, 1801, was the first to be held in the nation's new capital, Washington, D.C. That morning an artillery company on Capitol Hill had fired shots to welcome the daybreak, and in a first for a newspaper, Jefferson gave a copy of his speech to the National Intelligencer for it to be published and available right after delivery. He delivered a 1721-word speech in the United States Capitol's Senate Chamber. He was not a strong speaker, and the audience could barely catch his words, which called for national unity. The speech was widely reprinted and celebrated by Democratic-Republicans across the country as a clear statement of the party's principles.Peterson, 1970, pp. 655–59. The presidential oath of office was administered by Chief Justice John Marshall. Outgoing President Adams had left the capital earlier that day, and did not attend the ceremony.Appleby, 2003, pp. 5–6

Administration

Cabinet

By July 1801, Jefferson had assembled his cabinet, which consisted of Secretary of State James Madison, Secretary of the Treasury Albert Gallatin, Secretary of War Henry Dearborn, Attorney General Levi Lincoln Sr., and Secretary of the Navy Robert Smith. After his decision to pursue the presidency in the contingent election, Burr was excluded from any role in the Jefferson administration. Jefferson sought to make collective decisions with his cabinet, and each member's opinion was elicited before Jefferson made major decisions.Appleby, 2003, pp. 37–41 Gallatin and Madison were particularly influential within Jefferson's cabinet; they held the two most important cabinet positions and served as Jefferson's key lieutenants.McDonald, 1976, pp. 36–38

Patronage and the Federalists When Adams took office in 1797, he carried many of outgoing President George Washington's supporters over into his new administration. As a result, there was little change in the federal government during the transition between Washington and Adams, the first presidential transition in U.S. history. With Jefferson's election in 1800, there was a transfer of power between parties, not simply a transition between presidents. As president, Jefferson had the power of appointment to fill many government positions that had long been held by Federalists. Jefferson resisted the calls of his fellow Democratic-Republicans to remove all Federalists from their appointed positions, but he felt that it was his right to replace the top government officials, including the cabinet. He also replaced any lower-ranking Federalist appointees who engaged in misconduct or partisan behavior. Jefferson's refusal to call for a complete replacement of federal appointees under a "spoils system" was followed by his successors until the election of Andrew Jackson in 1828.Appleby, 2003, pp. 31–39

Judiciary

In the final days of his presidency, Adams had appointed numerous federal judges to fill positions created by the Judiciary Act of 1801. Democratic-Republicans were outraged by the appointment of these "midnight judges," almost all of whom were Federalists. Jefferson and his allies sought to reverse the Judiciary Act of 1801, partly because they did not believe the new judicial positions were necessary, and partly to weaken Federalist influence on the courts. Federalists vehemently opposed this plan, arguing that Congress did not have the power to abolish judicial positions that were occupied. Despite these objections, the Democratic-Republicans passed the Judiciary Act of 1802, which largely restored the judicial structure that had prevailed prior to the Judiciary Act of 1801.Appleby, 2003, pp. 7–8, 61–63 The Jefferson administration also refused to deliver judicial commissions to some Adams appointees who had won Senate confirmation but had not yet formally taken office. One such appointee, William Marbury, sued Secretary of State Madison to compel him to deliver the judicial commissions. In the 1803 Supreme Court case of Marbury v. Madison, the court ruled against Marbury, but also established the precedent of judicial review, thereby strengthening the judicial branch.

Still unhappy with Federalist power on the bench even after the passage of the Judiciary Act of 1802, the Democratic-Republicans impeached district court Judge John Pickering and Supreme Court Justice Samuel Chase. Federalist congressmen strongly opposed both impeachments, criticizing them as attacks on judicial independence. Pickering, who frequently presided over cases while drunk, was convicted by the Senate in 1804. However, the impeachment proceedings of Chase proved more difficult. While serving on the Supreme Court, Chase had frequently expressed his skepticism of democracy, predicting that the nation would "sink into mobocracy," but he had not shown himself to be incompetent in the same way that Pickering had. Several Democratic-Republican senators joined the Federalists in opposing Chase's removal, and Chase would remain on the court until his death in 1811. Though Federalists would never regain the political power they had held during the 1790s, the Marshall Court continued to reflect Federalist ideals until the 1830s.Appleby, 2003, pp. 65–69