Separation of church and state is not in the Constitution. The first amendment reads as follows:
Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the government for a redress of grievances.
The phrase comes directly from a letter written by Thomas Jefferson in 1802 to the Danbury Baptists Association.
Originally Posted by Thomas Jefferson
I contemplate with sovereign reverence that act of the whole American people which declared that their legislature should "make no law regarding an establishment of religion, or prohibiting the free exercise thereof," thus building a wall of separation between Church and State.
In 1947, regarding Everson v Board of Education, Justice Hugo Black wrote, "In the words of Jefferson, the clause against establishment of religion by law was intended to erect 'a wall of separation between church and state.'" It is only in recent times that separation has come under attack by judges in the federal court system who oppose separation of church and state."
The quote has been used in Supreme Court decisions a handful of times, and it is federal law.
This is part of what makes the gay marriage amendment so absurd. The prohibition of homosexual relationships comes directly from religious texts. The government should not be in the business of enforcing scripture.