When Madison proposed a Bill of Rights before the First Congress in 1789, he offered language that would protect the free exercise of religion and prohibit the establishment of a national church:
The civil rights of none shall be abridged on account of religious belief or worship, nor shall any national religion be established, nor shall the full and equal rights of conscience be in any manner, or on any pretext, infringed.
Madison also hoped the federal government would be granted the power to protect citizens against religious discrimination committed by their own state governments. He therefore proposed that, in addition to the limitations placed on Congress in Article I, Section 9, they should also add to Section 10 (which placed limits on state powers) the words: “No state shall violate the equal rights of conscience.” Madison did not even try to apply an “establishment” clause to state governments (almost half of which already had established churches). During the debates over guaranteeing the rights of conscience from state intrusion, Madison insisted that he believed this provision was “the most valuable amendment in the whole list.” Madison won his battle to prohibit the states from violating the rights of conscience in the House, but the Senate struck down the amendment. Therefore, the Bill of Rights submitted to the states for ratification contained only prohibitions on Congress’ power to interfere with religious freedom; the states were left in the same condition they had been prior to the passage of the 1st Amendment.