Thomas Jefferson was a man of deep religious conviction — his conviction was that religion was a very personal matter, one which the government had no business getting involved in. He was vilified by his political opponents for his role in the passage of the 1786 Virginia Statute for Religious Freedom and for his criticism of such biblical events as the Great Flood and the theological age of the Earth. As president, he discontinued the practice started by his predecessors George Washington and John Adams of proclaiming days of fasting and thanksgiving. He was a staunch believer in the separation of church and state.
Jefferson wrote a letter to the Danbury Baptist Association in 1802 to answer a letter from them written in October 1801. A copy of the
Danbury letter is available here. The Danbury Baptists were a religious minority in Connecticut, and they complained that in their state, the religious liberties they enjoyed were not seen as immutable rights, but as privileges granted by the legislature — as "favors granted." Jefferson's reply did not address their concerns about problems with state establishment of religion — only of establishment on the national level. The letter contains the phrase "wall of separation between church and state," which led to the short-hand for the Establishment Clause that we use today: "Separation of church and state."
) There is a pretty good mini history of that here:
