The principle of the separation of church and state in the United States has its roots in the nation's early history. Many of the original colonists were religious dissenters and minorities fleeing persecution in Europe. As a result, there was a strong sentiment among them that the government should not be able to interfere in matters of faith, to prevent the kinds of religious oppression they had experienced in their home countries.

This sentiment was encapsulated in the First Amendment to the US Constitution, which states: "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof...". This text is usually interpreted as having two clauses: the Establishment Clause (prohibiting the federal government from establishing a national religion or favoring one religion over others) and the Free Exercise Clause (preventing the government from interfering with the free exercise of religion).

One of the key figures in defining this principle was Thomas Jefferson, who in 1802 wrote a letter to the Danbury Baptist Association in Connecticut. In this letter, Jefferson stated: "I contemplate with sovereign reverence that act of the whole American people which declared that their legislature should 'make no law respecting an establishment of religion, or prohibiting the free exercise thereof,' thus building a wall of separation between Church & State." It's from this "wall of separation" phrase that we get the modern term "separation of church and state."