Some important Baptist figures in the struggle for separation of church and state were John Smyth, Thomas Helwys, Edward Wightman, Leonard Busher, Roger Williams (who was a Baptist for a short period but became a seeker), John Clarke, Isaac Backus, and John Leland.

In 1612 John Smyth wrote, "the magistrate is not by virtue of his office to meddle with religion, or matters of conscience". That same year, Thomas Helwys wrote that the King of England could "comaund what of man he will, and wee are to obey it," but concerning the church -- "with this Kingdom, our lord the King hath nothing to do." In 1614, Leonard Busher wrote what is believed to be the earliest Baptist treatise dealing exclusively with the subject of religious liberty.

The Danbury Baptist Association of Danbury, Connecticut sent a letter, dated October 7, 1801, to the newly elected President Thomas Jefferson, expressing concern over the lack in their state constitution of explicit protection of religious liberty, and against government establishment of religion. As a religious minority in Connecticut, the Danbury Baptists were concerned that a religious majority might "reproach their chief Magistrate..

Thomas 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. Quoting the First Amendment of the United States Constitution, he 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."