Of all the Founders, no one placed his philosophical mark on the new nation of the United States more than Thomas Jefferson (James Madison was a close second). Jefferson was truly a son of the Enlightenment embracing deism without reservation and rejecting traditional expressions of Christianity without reservation.
Like most deists, Jefferson did not believe that God was intimately involved in human affairs, and Christian doctrines that explicitly stated so, like the Incarnation, the authority of Scripture, and resurrection were to be rejected as the "deliria of crazy imaginations." Jefferson referred to the doctrine of the Trinity as "mere abracadabra." (1) Jefferson did, however, believe that individuals would be judged by God for their deeds, though the idea of any kind of eternal state of damnation was anathema. (2) For Jefferson, like other deists, the chief contribution of religion was to make moral people and good citizens. Doctrine was irrelevant. Jefferson did suggest, however, that on rare occasions God might answer prayer.
Jefferson did not have a very high view of the clergy as a profession. Throughout his life he referred to all clergy, including Protestant pastors as "priests." The term, in his context, was not a compliment. Jefferson believed that priests like kings were enemies of individual freedom, and that such doctrines as the Trinity were simply used by the clergy to retain their manipulative power over the people. In a letter to John Adams, Jefferson wrote, "It is too late in the day for men of sincerity to pretend they believe in the Platonic mysticisms that three are one, and one is three; and yet that the one is not three, and the three are not one.... But this constitutes the craft, power, and the profit of the priests." (3) Jefferson believed that the power the clergy exercised historically in Europe and the colonies was enough of an argument to exclude them from holding public office. It must be said, however, that while Jefferson was distrustful of the clergy as an institution (especially Catholic priests... Jefferson had little good to say about Catholicism), he did speak well of individual "priests" who did much charitable good in the community, and he was good friends with a liberal minister and scientist, Joseph Priestly.
Jefferson loved what he called the good and simple religion of Jesus. His problem was not with Jesus but with how, so he believed, his followers distorted his teaching. The two Christian figures Jefferson reserved his harshest literary venom for was St. Paul and John Calvin. For Jefferson, Paul turned Jesus, the great moral deistic teacher (Jefferson actually referred to Jesus as a deist) into a divine Savior who redeemed the world in slaughterhouse fashion for a blood-thirsty deity. Calvin adds to Paul's distortion of Jesus with his doctrine of original sin, which erroneously claimed humanity's helplessness before God, and double-predestination in which God decided by fiat who was to saved and who was to be damned. (4) Jefferson found all of this to be absurd.
Jefferson's most well known views on religion were his thoughts he offered on the Bible itself. Jefferson embraced the teaching of Jesus as simple enough to be understood by a child, but rejected what he could not stomach (his words) as the unreasonable parts of Scripture, particularly the Gospels' stories of miracles including the resurrection. Near the end of his life, though it was a project started years before while he was president, Jefferson took scissors to the Gospels and cut out the parts of the four Gospels he believed to be the authentic teachings of Jesus and arranged them into a narrative of the "most pure, benevolent, and sublime [teachings] which have ever been preached to man." He did not allow the work to be published during his life. It was after his death. The final work, which came to be known as The Jefferson Bible is still in print to this day.
Jefferson was extremely concerned with practice or ritual of government which undermined his exclusionary understanding of the separation of church and state. Both Presidents Washington and Adams had proclaimed national days of prayer, fasting, and thanksgivings. Jefferson stopped the practice during his administration because he said it was "too Christian a thing for the president to do." (5)
Toward the end of his life, Jefferson started to speak of God in more personal terms. While he continued to use the preferred deistic language of Providence and Creator, he began to refer to the deity as "God" and even "my God." In his old age attending worship (Jefferson was always fairly active in church attendance), witnesses noted that Jefferson frequently teared up as the old hymns were sung. It would be foolish to conclude from this that Jefferson began to embrace the doctrines expressed in those hymns that deists considered to be outdated, since there is nothing in his later writings that remotely hint at such a thing. Rather, it was more likely the sentimental reminiscing of an old man who remembered singing those same hymns as a young boy with his sister by the light of the evening fire. (6)
Like John Adams, Thomas Jefferson affirmed an afterlife where he would be joining his loved ones and emphasized that eternity the older he became.
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I do not seek to understand that I may believe, but I believe in order to understand. For this also I believe, –that unless I believed, I should not understand.-- St. Anselm of Canterbury (1033-1109)