On matters of religion, Jefferson in 1800 was accused by his political opponents of being an atheist and enemy of religion. But Jefferson wrote at length on religion and many scholars agree with the claim that Jefferson was a deist, a common position held by intellectuals in the late 18th century. As Avery Cardinal Dulles, a leading Roman Catholic theologian reports, "In his college years at William and Mary he [Jefferson] came to admire Francis Bacon, Isaac Newton, and John Locke as three great paragons of wisdom. Under the influence of several professors he converted to the deist philosophy."[22] Dulles concludes:
“ In summary, then, Jefferson was a deist because he believed in one God, in divine providence, in the divine moral law, and in rewards and punishments after death; but did not believe in supernatural revelation. He was a Christian deist because he saw Christianity as the highest expression of natural religion and Jesus as an incomparably great moral teacher. He was not an orthodox Christian because he rejected, among other things, the doctrines that Jesus was the promised Messiah and the incarnate Son of God. Jefferson's religion is fairly typical of the American form of deism in his day. ”
Biographer Merrill Peterson summarizes Jefferson's theology:
“ First, that the Christianity of the churches was unreasonable, therefore unbelievable, but that stripped of priestly mystery, ritual, and dogma, reinterpreted in the light of historical evidence and human experience, and substituting the Newtonian cosmology for the discredited Biblical one, Christianity could be conformed to reason. Second, morality required no divine sanction or inspiration, no appeal beyond reason and nature, perhaps not even the hope of heaven or the fear of hell; and so the whole edifice of Christian revelation came tumbling to the ground.[23] ”
Jefferson used deist terminology in repeatedly stating his belief in a creator, and in the United States Declaration of Independence used the terms "Creator", "Nature's God". Jefferson believed, furthermore, it was this Creator that endowed humanity with a number of inalienable rights, such as "life, liberty, and the pursuit of happiness". His experience in France just before the French Revolution made him deeply suspicious of Catholic priests and bishops as a force for reaction and ignorance. Similarly, his experience in America with inter-denominational intolerance served to reinforce this skeptical view of religion. In a letter to Willam Short, Jefferson wrote: "the serious enemies are the priests of the different religious sects, to whose spells on the human mind its improvement is ominous."[24]
Jefferson was raised in the Church of England, at a time when it was the established church in Virginia and only denomination funded by Virginia tax money. Before the Revolution, Jefferson was a vestryman in his local church, a lay position that was part of political office at the time. He also had friends who were clergy, and he supported some churches financially. During his Presidency, Jefferson attended the weekly church services held in the House of Representatives. Jefferson later expressed general agreement with his friend Joseph Priestley's Unitarianism, that is the rejection of the doctrine of Trinity. In a letter to a pioneer in Ohio he wrote, "I rejoice that in this blessed country of free inquiry and belief, which has surrendered its conscience to neither kings or priests, the genuine doctrine of only one God is reviving, and I trust that there is not a young man now living in the United States who will not die a Unitarian."[25]
Jefferson did not believe in the divinity of Jesus, but he had high esteem for Jesus' moral teachings, which he viewed as the "principles of a pure deism, and juster notions of the attributes of God, to reform [prior Jewish] moral doctrines to the standard of reason, justice & philanthropy, and to inculcate the belief of a future state."[26] Jefferson did not believe in miracles. He made his own condensed version of the Gospels, omitting Jesus' virgin birth, miracles, divinity, and resurrection, primarily leaving only Jesus' moral philosophy, of which he approved. This compilation was published after his death and became known as the Jefferson Bible.
“ [The Jefferson Bible] is a document in proof that I am a real Christian, that is to say, a disciple of the doctrines of Jesus, very different from the Platonists, who call me infidel and themselves Christians and preachers of the gospel, while they draw all their characteristic dogmas from what its author never said nor saw.[27] ”
In spite of evidence pointing to a life of deism or progressive Christianity, however, it has been suggested by polemicist Christopher Hitchens that at the end of his days, Jefferson's leanings may have been closer to that of an atheist. Hitchens cites several of Jefferson's letters to friends as he approached his death, stating that he awaited his end without "either hope or fear". Hitchens also notes an earlier correspondence with nephew Peter Carr, cautioning against shying away from confronting the possible absence of a god due to "any fear of its consequences."[28] Though an individual's inner feelings can never truly be known, these correspondences could indicate a gulf between his public and private religious leanings.