While most recognize the phrase "separation of church and state," few know its source; but it is important to understand the origins of that phrase. What is the history of the First Amendment?
The process of drafting the First Amendment made the intent of the Founders abundantly clear; for before they approved the final wording, the First Amendment went through nearly a dozen different iterations and extensive discussions.
Those discussions—recorded in the Congressional Records from June 7 through September 25 of 1789—make clear their intent for the First Amendment. By it, the Founders were saying: "We do not want in America what we had in Great Britain: we don’t want one denomination running the nation. We will not all be Catholics, or Anglicans, or any other single denomination. We do want God’s principles, but we don’t want one denomination running the nation."
This intent was well understood, as evidenced by court rulings after the First Amendment. For example, a 1799 court declared:
"By our form of government, the Christian religion is the established religion; and all sects and denominations of Christians are placed on the same equal footing."
Again, note the emphasis: "We do want Christian principles—we do want God’s principles—but we don’t want one denomination to run the nation."
In 1801, the Danbury Baptist Association of Danbury, Connecticut, heard a rumor that the Congregationalist denomination was about to be made the national denomination. That rumor distressed the Danbury Baptists, as it should have. Consequently, the fired off a litter to President Thomas Jefferson voicing their concern. On January 1, 1802, Jefferson wrote the Danbury Baptists, assuring them that "the First Amendment has erected a wall of separation between church and state."
His letter explained that they need not fear the establishment of a national denomination—and that while the wall of the First Amendment would protect the church from government control—there always would be open and free religious expression of all orthodox religious practices, for true religious expression of all orthodox religious practices, for true religious duties would never threaten the purpose of government. The government would interfere with a religious activity was a direct menace to the government or to the overall peace and good order of society. (Later Supreme Court identified potential "religious" activities in which the government might interfere: things like human sacrifice, bigamy or polygamy, the advocation of immorality or licentiousness, etc. If any of these activities were to occur in the name of "religion," then the government would interfere, for these were activities which threaten public peace and safety; but with orthodox religious practices, the government would not interfere).
Today, all that is heard of Jefferson’s letter is the phrase, "a wall of separation between church and state," without either the context, or the explanation given in the letter, or its application by earlier courts. The clear understanding of the First Amendment for a century-and-a-half was that it prohibited the establishment of a single national denomination. National policies and rulings in that century-and-a-half always reflected that interpretation.
For example, in 1853, a group petitioned Congress to separate Christian principles from government. They desired a so-called "separation of church and state" with chaplains being turned out of the congress, the military, etc. Their petition was referred to the House and the Senate Judiciary Committees, which investigated for almost a year to see if it would be possible to separate Christian principles from government.
Both the House and the Senate Judiciary Committees returned with their reports. The following are excerpts from the House report delivered on Mary 27, 1854 (the Senate report was very similar):
"Had the people [the Founding Fathers], during the Revolution, had a suspicion of any attempt to war against Christianity, that Revolution would have been strangled in its cradle. At the time of the adoption of the Constitution and the amendments, the universal sentiment was that Christianity should be encouraged, but not any one sect [denomination]…. In this age, there is no substitute for Christianity…. That was the religion of the founders of the republic, and they expected it to remain the religion of their descendants."
Two months later, the Judiciary Committee made this strong declaration:
"The great, vital, and conservative element in our system [the thing that holds our system together] is the believe of our people in the pure doctrines and divine truths of the Gospel of Jesus Christ."
The Committees explained that they would not separate these principles, for it was these principles and activities which had made us so successful—they had been our foundation, our basis.
During the 1870s, 1880s, and 1890s, yet another group which challenged specific Christian principles in government arrived before the Supreme Court. Jefferson’s letter had remained unused for years, for as time had progressed after its use in 1802—and after no national denomination had been established—his letter had fallen into obscurity. But now—75 years later—in the case Reynolds v. United States, the plaintiffs resurrected Jefferson’s letter, hope to use it to their advantage.
In that case, the Court printed an lengthy segment of Jefferson’s letter and then used his letter on "separation of church and state" to again prove that it was permissible to maintain Christian values, principles, and practices in official policy. For the next 15 years during that legal controversy, the Supreme Court utilized Jefferson’s letter to ensure that Christian principles remained a part of government.
Following this controversy, Jefferson’s letter again fell into disuse. It then remained silent for the next 70 years until 1947, when, in Everson v. Board of Education, the Court, for the first time, did not cite Jefferson’s entire letter, but selected only eight words from it. The Court now announced:
"The First Amendment has erected ‘a wall of separation between church and state.’ That wall must be kept high and impregnable."