Day of Thanksgiving and Prayer
From Thomas Jefferson Encyclopedia
It is popular belief that Jefferson wrote proclamations for a Day of Thanksgiving and Prayer. While Governor of Virginia, the Continental Congress sent a circular to the state executives recommending a day of public thanksgiving. He sent the circular to the Virginia House of Delegates which wrote out the actual proclamation and sent it for his signature. Jefferson did sign this proclamation to be held on December 9, 1779. It must be remembered that the governor of Virginia at this time was a weak office. The General Assembly formulated policy, not the governor. This proclamation did not establish a permanent annual observance. So it's true that he had the proclamation issued, but it was not necessarily his idea.
When Jefferson was President, he was even more hesitant to even issue proclamations of this sort. Jefferson writes in a letter to Reverend Samuel Miller on January 23, 1808, in response to Miller's proposal that he "recommend" a national day of fasting and prayer: "I consider the government of the United States as interdicted by the Constitution from inter meddling with religious institutions, their doctrines, discipline, or exercises...Certainly no power to prescribe any religious exercise, or to assume authority in religious discipline, has been delegated to the general government. ...But it is only proposed that I should recommend, not prescribe a day of fasting and prayer. That is, that I should indirectly assume to the United States an authority over religious exercises, which the Constitution has directly precluded them from...civil powers alone have been given to the President of the United States and no authority to direct the religious exercises of his constituents."