All Northern organizations acted in 1865 upon the assumption that a reunion of the churches must take place and that the divisions existing before the war should not be continued, since slavery, the cause of the division, had been destroyed. But they insisted that the reunion must take place upon terms named by the "loyal" churches, that the Negroes must also come under "loyal" religious direction, and that tests must be applied to the Confederate sinners asking for admission, in order that the enormity of their crimes should be made plain to them. But this policy did not succeed. The Confederates objected to being treated as "rebels and traitors" and to "sitting upon stools of repentance" before they should be received again into the fold.

Only two denominations were reunited--the Methodist Protestant, the northern section of which came over to the southern, and the Protestant Episcopal, in which moderate counsels prevailed and into which Southerners were welcomed back. The Southern Baptists maintained their separate existence and reorganized the Southern Baptist Convention, to which came many of the Baptist associations in the Border States; the Catholcs did not divide before 1861 and therefore had no reconstruction problems to solve; and the smaller denominations maintained the organizations which they had before 1861. A Unionist preacher testified before the Joint Committee on Reconstruction that even the Southern Quakers "are about as decided in regard to the respectability of secession as any other class of people."