|The Constitutional Principle: Separation of Church and State|
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Douglass Adair, who edited James Madison's Autobiography, wrote in his Preface to the volume:
No one who reads the Autobiography can fail to gain a new perspective, for example, on the part Madison played in furthering the establishment of religious liberty in America as "a natural and absolute right." The catalogue of incidents which testify to his deep devotion to the cause runs through the memoir like a minor theme, beginning with his defense of the Orange County Baptists in the 1770's and continuing through his earnest warning against the dangers of "mingling" religion and politics in presidential proclamations. It is no exaggeration to say that none of Madison's other writings on the subject reveals so clearly his life-long effort to bring about a complete and absolute separation of church and state in this country. Nor can any reader of the Autobiography, noting the Virginian's scruples about the salary paid the Chaplain of Congress ("a violation of principle") and his qualms as President about issuing the call for a "day of Religious Service during the War of 1812, fail to realize that Madison was slightly pedantic in applying his abstract principle of separation to specific situations. This doctrinaire quality of the Virginian's religious liberalism, as well as his confessed distaste for the theological "enthusiasm" of the Baptists ("obnoxious to sober opinion") whom he fought to protect, merely shows, of course, that Madison always approached the problem of religious freedom as a typical "philosophic" statesman of the eighteenth century enlightenment.
Excerpts from James Madison's Autobiography
[Note that James Madison dictated his autobiography in the third person]
On the commencement of the dispute with Great Britain, he entered with the prevailing zeal into the American Cause; being under very early and strong impressions in favour of Liberty both Civil & Religious. His devotion to the latter found a particular occasion for its exercise in the persecution instituted 12 in his County  as elsewhere against the preachers belonging to the sect of Baptists shell beginning to spread thro' the Country. Notwithstanding the enthusiasm which contributed to render them obnoxious to sober opinion as well as to the laws then in force, against Preachers dissenting from' the Established Religion, he spared no exertion to save them from imprisonment & to promote their release from it. This interposition tho' a mere duty prescribed by his conscience, obtained for him a lasting place in the favour of that particular sect. Happily it was not long before the fruits of Independence and of the spirit & principles which led to it, included a complete establishment of the Rights of Conscience, without any distinction of sects or individuals.
In the spring of 1776 he was initiated into the political career by a County election to the convention, which formed the original Constitution of the State with the Declaration of Rights prefixed to it; and which on the 16th day of May unanimously instructed her deputies in Congress to propose the final separation from G. Britain, as declared by that Body on the 4th of July following. Being young & in the midst of distinguished and experienced members of the Convention he did not enter into its debates; tho' he occasionally suggested amendments; the most material of which was a change of the terms in which the freedom of Conscience was expressed in the proposed Declaration of Rights This important an meritorious instrument was drawn by Geo. Mason. who had inadvertently adopted the word toleration13 in the article on that subject. The change suggested and accepted, substituted a phraseology which - declared the freedom of conscience to be a natural and absolute13 right.
He was accordingly elected in the spring of 1784 & reelected for the twosuccessive years. For the Legislative proceedings of Virginia during that interesting period, embracing the Convention at Annapolis - the proposed grant of power to Congress and its recommendation of that at Philadelphia - the project of a Religious Establishment - the separation of Kentucky from  Virginia - the effort for paper money - the revised code of laws prepared by the case of British debts - the offered and declined donation to Genl. Washington - the attempted one to Thos. Paine &c- see his correspondence with Genl W.- Edd R. and particularly the copious one with Mr Jefferson during that period. See also the Memorial & Remonstrance against the Religious Establishment, and an explanatory letter to Geo. Mason of Green Spring - notes of the proceedings at Annapolis, and an explanatory correspondence with Noah Webster as to the origin of the Convention there. In the statement prefixed to the laws of U. S. edited by Rush and Colvin, there is an error in ascribing the Resolutions of Va - in 1785, there cited, to J. Madison. They were the Report of a Committee on his, which varied them from a longer duration to 8 years. This circumstance contributed to the abandonment of them.
He was much surprized and disappointed at the incompleting of the Ratification of the prohibitory Article proposed to the Constitution of the U. S. in 1790, which he had eluded [sic] in the proposed amendments in 1790, and had much at heart.
He disapproved also of Chaplains to Congress paid out of the public Treasury-as a violation of principle. He thought the only legitimate and becoming mode would be that of voluntary contribution from the members. See remarks on the subject in his manuscript papers on file.
For his career in the Executive Magistracy-See State Papers-his correspondence with Heads of Departments, including instructions to them-his private correspondence with our ministers abroad-see particularly with Barlow, and his account of Buonaparte's sight of my letter to Barlow-his correspondence with Mr Jefferson-Mr Pendleton & others on his files. See statement of what passed with Rob. Smith, Eustis, Hamilton & Armstrong on their separation from their respective Departments- See also a publication of Armstrong in the Literary and Scientific Repository, and an exposure on file of its deceptive representation of the appointment of Genl Jackson to a command in the regular Army. See also the ground on which he recommended, in compliance with multiplied applications, the Proclamation of a day for Religious Service; the ground being a voluntary concurrence of those who approved a general union on such an occasion, for which the mere intimation of a day would be sufficient. See the danger of mingling political & even party views with such Proclamation in the Remarks of Hamilton on the Proclamation drafted for Genl Washington by Edmund Randolph. The files of the Department of State contain the original draft with the notes referred to. A copy from the office of State is among the papers of J. Madison. For the origin of the war & its preparations and early operations, see letter to H. Wheaton Feby. 26. 1827.
"Notes And Documents: James Madison's Autobiography," Edited by Douglass Adair Madison College Library Harrisonburg, Virginia Reprinted From The William and Mary Quarterly, 3d Ser., 11 (April 1945)*