Separation of church and state is a liberal interpretation of the Establishment Clause of the United States Constitution, an interpretation particularly favored by atheists. The section in question is the First Amendment, which reads "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.".  This phrase has been interpreted by some judges to exclude religion from Government by declaring that Church and state must be kept separate. Conservatives have long criticized this interpretation as being without justification in the text or meaning of the First Amendment.
The founding fathers had also included a provision for separating the undue influence of religion from the government in the original United States Constitution. Article VI, Debts, Supremacy, Oaths, states "The Senators and Representatives before mentioned, and the Members of the several State Legislatures, and all executive and judicial Officers, both of the United States and of the several States, shall be bound by Oath or Affirmation, to support this Constitution; but no religious Test shall ever be required as a Qualification to any Office or public Trust under the United States."
Keeping the State from the Church's Influence
Thomas Jefferson, the least religious of the Founding Fathers and one of the few who played no role in the drafting of the U.S. Constitution or the First Amendment, first coined the phrase as president in 1802 - a decade after the First Amendment was ratified.. Jefferson used the phrase to appease the Danbury Baptist Association rather than recite an objective interpretation of the law. At the end of his letter, in reflection of how Jefferson himself did not interpret his own phrase to exclude religion from government, he expressed prayers for the letter's recipients:
- To messers. Nehemiah Dodge, Ephraim Robbins, & Stephen S. Nelson, a committee of the Danbury Baptist association in the state of Connecticut.
- The affectionate sentiments of esteem and approbation which you are so good as to express towards me, on behalf of the Danbury Baptist association, give me the highest satisfaction. my duties dictate a faithful and zealous pursuit of the interests of my constituents, & in proportion as they are persuaded of my fidelity to those duties, the discharge of them becomes more and more pleasing.
- Believing with you that religion is a matter which lies solely between Man & his God, that he owes account to none other for his faith or his worship, that the legitimate powers of government reach actions only, & not opinions, 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. Adhering to this expression of the supreme will of the nation in behalf of the rights of conscience, I shall see with sincere satisfaction the progress of those sentiments which tend to restore to man all his natural rights, convinced he has no natural right in opposition to his social duties.
- I reciprocate your kind prayers for the protection & blessing of the common father and creator of man, and tender you for yourselves & your religious association, assurances of my high respect & esteem.
- Th Jefferson
- Jan. 1. 1802 
The Treaty of Tripoli, drafted during Washington's presidency, ratified by unanimous vote of the Senate June 7th, 1797  and signed by John Adams three days later, states that "As the government of the United States of America is not in any sense founded on the Christian Religion,-as it has in itself no character of enmity against the laws, religion or tranquility of Musselmen (Muslims),-and as the said States never have entered into any war or act of hostility against any Mehomitan nation (Islamic), it is declared by the parties that no pretext arising from religious opinions shall ever produce an interruption of the harmony existing between the two countries" Many proponents of a Christian America point out that the treaty was superseded by the Treaty of Peace and Amity in 1805 when the United States had more of an upper hand against the pirates. It has also been noted that since the war was against an Islamic regime, that the United states did not want to make it seem like it was a Crusade of Christianity against Islam, but rather that the kidnapping actions of the government regardless of their religious views was what was being objected to.
Separating the Church from the State's Influence
Like many political doctrines, the separation of church & state is a double-edged sword. If religion cannot influence government, nor can government influence religion. Accordingly, churches and religious organizations are kept from government intrusion with the highest deference to ecclesiastical matters. For example, Title VII contains a built-in exception for religious organizations. The provision has been construed to allow churches to handle their ministerial matters without government intrusion in any way. In this sense, separation of church & state is good for the church, as it ensures religious autonomy.
Only a Limit on Federal Power
Pat Robertson has argued that the Establishment Clause was intended merely to prevent the Federal government from imposing a state religion, as many of the original 13 states already had their own official religion.
- Let's look again at the constitution's intent to empower the legislature. With Congress holding such power, the states got nervous. They reasoned that relinquishing so much power to the Congress threatened state sovereignty. After all, this is a United States of America. It is not one vast democracy of homogeneous people. It is Maryland. It is Connecticut. It is Massachusetts. It is New York. These are separate states. So the Constitution was enhanced by the Bill of Rights. The first point in the Bill of Rights, the First Amendment to the Constitution, said "Congress shall pass no law respecting the establishment of religion or prohibiting the free exercise thereof." There were certain states at that time that had established religions. Massachusetts was a case in point. They had a state religion. And they didn't want this enormously powerful Congress to superimpose a religious system on their state system. To guarantee the states retained critical rights, the tenth amendment said, "All the power that is not expressly delegated to the federal government is reserved for the states." The intent? The people, i.e. the states, have delegated power. They gave up some powers, but they did not give up all powers because they are sovereign states.
- Pat Robertson, Yale University Law School, March 25, 1986
- 1st Amendment of the US Constitution
- See, e.g. Lemon v. Kurtzman.
- Religion and the Federal Government, LOC.gov
- Letter from Thomas Jefferson to the DBA
- Journal of the executive proceedings of the Senate of the United States of America, 1789-1805
- Treaty of Tripoli, Article 11. Ratified in 1796 and again in 1797.
- 42 U.S.C. 2000(e)-(1).
- McClure v. Salvation Army.