Jefferson first ran for President of the United States in 1796, and he came in second place after John Adams. Under the electoral rules of the time, he became vice president.
Historians say it was a tumultuous four years. According to some accounts, Jefferson and Adams never communicated during the entire administration.
In 1800, Jefferson ran against Adams again for the presidency, and Jefferson's lack of faith was a central issue. The Adams campaign displayed posters declaring, "John Adams and God or Jefferson and no God!"
When the votes were cast, Jefferson dominated the Southern region of the country while Adams dominated the North. The vote in the Electoral College tied, and it was thrown into the House of Representatives where the chamber voted 29 times before making Jefferson president.
Danbury Baptists
Politics has changed little since the founding of the country, and those who had voted for Adams considered Jefferson to be an illegitimate president. One group of Baptists in Danbury, Connecticut, sought to catch Jefferson in a politically embarrassing situation.
Although presidents write them perfunctorily now, Thanksgiving Day proclamations were highly controversial at the time, so the Danbury Baptists wrote Jefferson asking him to declare one.
Jefferson, a shrewd politician, wrote back saying that it was out of his purview to do such things because the Constitution had created a "wall of separation between church and state." Rather than take the issue head on, Jefferson ducked.
Everson vs. Board of Education
The phrase "separation of church and state" would not become part of the national jurisprudence until the Supreme Court decided Everson vs. Board of Education in 1947. Claimants asked the court to decide whether tax revenues could be used to transport students to private Catholic schools.
Although the court sided with the students since schooling had a distinctly secular purpose, Justice Hugo Black wrote the following in his majority opinion. "The First Amendment has erected a wall between church and state. That wall must be kept high and impregnable."
Since then the court has been asked to decide many other matters related to the wall of separation.