On October 7, 1801, the Danbury Baptist Association of Danbury, Connecticut sent a letter to the newly elected President Thomas Jefferson, expressing concern over the lack in their state constitution of explicit protection of religious liberty, and against a government establishment of religion. At the time, they were being persecuted because they did not belong to the Congregationalist establishment in Connecticut.
In their letter to the President, the Danbury Baptists affirmed that “Our Sentiments are uniformly on the side of Religious Liberty — That Religion is at all times and places a matter between God and individuals — That no man ought to suffer in name, person, or effects on account of his religious Opinions — That the legitimate Power of civil government extends no further than to punish the man who works ill to his neighbor…”.
As a religious minority in Connecticut, the Danbury Baptists were concerned that a religious majority might “reproach their chief Magistrate… because he will not, dare not assume the prerogatives of Jehovah and make Laws to govern the Kingdom of Christ,” thus establishing a state religion at the cost of the liberties of religious minorities.
Some individuals and groups assert that the Baptists wrote to Jefferson because they wanted him to issue a proclamation calling for a day of fasting and prayer or because they were alarmed over a rumor they had heard that a national church was about to be established. These assertions are not accurate. The Baptists wrote to Jefferson to commend him for his stand in favor of religious liberty and to express their dissatisfaction with the church-state relationship in Connecticut. Jefferson himself did not view his response as a minor, unimportant letter; he had it reviewed by Levi Lincoln, his attorney general, before he sent it. Jefferson told Lincoln that he considered this letter to be a means of “sowing useful truths and principles among the people, which might germinate and become rooted among their political tenets.”
Jefferson’s response, dated January 1, 1802, concurs with the Danbury Baptists’ views on religious liberty, and the accompanying separation of civil government from concerns of religious doctrine and practice. Jefferson writes: “…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”.
U. S. Supreme Court decisions through the past two centuries repeatedly refer to Jefferson’s writings as instructive in how to interpret all facets of the Constitution, not merely with regards to First Amendment issues — but those issues do receive particular attention. In the 1879 decision Reynolds v. U.S., for example, the court observed that Jefferson’s writings “may be accepted as an authoritative declaration of the scope and effect of the [First] Amendment.”
The Supreme Court has often cited Jefferson’s Danbury letter in discussions of the original intent of the First Amendment. One of the most important cases was the landmark decision of Everson v. Board of Education of the Township of Ewing et al., 330 U.S. 1  in which the court ruled that the Fourteenth Amendment required that the First Amendment’s separation of church and state also applies to the states. This was the first Supreme Court case incorporating the Establishment Clause of the First Amendment as binding upon the states through the Due Process Clause of the Fourteenth Amendment. The decision in Everson marked a turning point in the interpretation and application of disestablishment law in the modern era. Although several justices dissented from the majority opinion in Everson, their argument was with whether the practice at issue in the case had in fact breached the “wall of separation.” Both affirming and dissenting Justices were decisive that the Constitution required a sharp separation between government and religion, and their strongly worded opinions paved the way to a series of later court decisions that taken together brought about profound changes in legislation, public education, and other policies involving matters of religion. Both Justice Hugo Black’s majority opinion and Justice Wiley Rutledge’s dissenting opinion defined the First Amendment religious clause in terms of a “wall of separation between church and state”. That the full court assumed that the First Amendment intended to separate church and state is evident from Justice Rutledge’s dissenting opinion which was endorsed by all the dissenting justices:
“The Amendment’s purpose was not to strike merely at the official establishment of a single sect, creed or religion, outlawing only a formal relation such as had prevailed in England and some of the colonies. Necessarily it was to uproot all such relationships. . . . But the object was broader than separating church and state in this narrow sense. It was to create a complete and permanent separation of the spheres of religious activity and civil authority by comprehensively forbidding every form of public aid or support for religion.”