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The statement about a wall of separation between church and state was made in a letter on January 1, 1802, by Thomas Jefferson to a church (the Danbury Baptist Association of Connecticut). The congregation heard a widespread rumor that the Congregationalists, another denomination, were to become the national religion. This was very alarming to people who knew about religious persecution in England by the state established church. Jefferson made it clear in his letter to the Danbury Congregation that the separation was to be that government would not establish a NATIONAL religion or dictate to men how to worship God. Jefferson's letter from which the phrase "separation of church and state" was written was to affirm first amendment rights.
The "wall" was understood as one-directional; its purpose was to protect the church from the state. The people did not want freedom FROM religion, but freedom OF religion.
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