Despite the contemporary claims that Jefferson and Madison were strict proponents of the concept of separation of church and state as it is currently presented in modern debate, it is a common misconception to assume that religion was not associated with the practice of politics in early American life. In fact, the Religion and the Founding of the American Republic website exhibit at the Library of Congress states,
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It is no exaggeration to say that on Sundays in Washington during the administrations of Thomas Jefferson (1801-1809) and of James Madison (1809-1817) the state became the church. Within a year of his inauguration, Jefferson began attending church services in the House of Representatives. Madison followed Jefferson's example, although unlike Jefferson, who rode on horseback to church in the Capitol, Madison came in a coach and four. Worship services in the House--a practice that continued until after the Civil War--were acceptable to Jefferson because they were nondiscriminatory and voluntary. Preachers of every Protestant denomination appeared. (Catholic priests began officiating in 1826.) As early as January 1806 a female evangelist, Dorothy Ripley, delivered a camp meeting-style exhortation in the House to Jefferson, Vice President Aaron Burr, and a "crowded audience." Throughout his administration Jefferson permitted church services in executive branch buildings. The Gospel was also preached in the Supreme Court chambers.[1]
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In fact, the Library of Congress exhibit clearly states that Jefferson apparently had no objection to non-discriminatory religion being practiced in state, but rather he objected ONLY to the formation of a state supported church – such as is practiced by Britain with her official recognition of the Church of England as the state church.[2]