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Thomas Jefferson was inaugurated the third president of the United States on March 4, 1801, following one of the most bitterly contested presidential elections in American history. He had faced the unpopular incumbent, Federalist John Adams of Massachusetts—his confrere in the independence struggle and longtime rival. The electorate was deeply divided along regional, partisan, and ideological lines. Acrimonious campaign rhetoric punctuated the polarized political landscape.

In few, if any, presidential contests has religion played a more divisive and decisive role than in the election of 1800. Jefferson's religion, or alleged lack thereof, emerged as a critical issue in the campaign. His Federalist opponents vilified him as a Jacobin and atheist. (Both charges stemmed from his notorious sympathy for the French Revolution, which in the 1790s had turned bloody and, some said, anti-Christian.) In the days before the election, the Gazette of the United States, a leading Federalist newspaper, posed the "grand question" of whether Americans should vote for "GOD—AND A RELIGIOUS PRESIDENT [John Adams]; or impiously declare for JEFFERSON—AND NO GOD!!!"

Jefferson's Federalist foes did not invent the stinging accusation that he was an infidel. Years before, his ardent advocacy for disestablishment in Virginia had led many pious Americans to conclude that Jefferson was, if not an enemy of religion, at least indifferent towards organized religion's vital role in civic life. The publication of his Notes on the State of Virginia in the mid-1780s exacerbated these fears. He wrote, "It does me no injury for my neighbor to say there are twenty gods, or no God. It neither picks my pocket nor breaks my leg." This passage came back to haunt him in the 1800 campaign. Detractors said this proved he was an infidel or, worse, an atheist.

Jefferson described himself as "a real Christian," although he was certainly aware that his beliefs were unconventional. "I am of a sect by myself," he said. He believed that human reason was the arbiter of religious truth and rejected key tenets of orthodox Christianity, including the Bible's divine origins, the deity of Christ, original sin, and the miraculous accounts in Scripture.

Despite his deviations from orthodoxy, he rejected suggestions that his views were of "that anti-Christian system imputed to me by those who know nothing of my opinions." His religion was very different, Jefferson conceded, from the leading churchmen of his day who called him an "infidel and themselves Christians and preachers of the gospel." He believed that Jesus Christ's moral teachings, stripped of the fiction and artifice carefully crafted by those calling themselves Christians, were "the most perfect and sublime that has ever been taught by man."

Jefferson's faith provided an early test of religion's place in national politics. His heterodox beliefs raised doubts about his fitness for high office. In 1798, Timothy Dwight, a Congregationalist minister and the president of Yale College, warned that the election of Jeffersonian Republicans might usher in a Jacobin regime in which "we may see the Bible cast into a bonfire, the vessels of the sacramental supper borne by an ass in public procession, and our children … chanting mockeries against God … [to] the ruin of their religion, and the loss of their souls."

In an influential pamphlet published in 1800, William Linn, a Dutch Reformed clergyman, warned that a vote for Jefferson "must be construed into no less than rebellion against God." He added ominously that the promotion of an infidel to high office would encourage public immorality and lead to the "destruction of all social order and happiness."

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