“I write nothing for publication, and last of all things should it be on the subject of religion. On the dogmas of religion as distinguished from moral principles, all mankind, from the beginning of the world to this day, have been quarrelling, fighting, burning and torturing one another, for abstractions unintelligible to themselves and to all others, and absolutely beyond the comprehension of the human mind. Were I to enter on that arena, I should only add an unit to the number of Bedlamites.[Letter to Mathew Carey, 11 November 1816]”

“When we see religion split into so many thousand of sects, and I may say Christianity itself divided into its thousands also, who are disputing, anathematizing and where the laws permit burning and torturing one another for abstractions which no one of them understand, and which are indeed beyond the comprehension of the human mind, into which of the chambers of this Bedlam would a man wish to thrust himself.[Letter to George Logan, 12 November 1816]”

“I am for freedom of religion, and against all maneuvers to bring about a legal ascendency of one sect over another.”

“If by religion we are to understand sectarian dogmas, in which no two of them agree, then your exclamation on that hypothesis is just, "that this would be the best of worlds if there were no religion in it.”

“The constitution of most of the states (and of the United States) assert that all power is inherent in the people; that they may exercise it by themselves; that it is their right and duty to be at all times armed and that they are entitled to freedom of person, freedom of religion, freedom of property, and freedom of the press.”

“That ideas should freely spread from one to another over the globe, for the moral and mutual instruction of man, and improvement of his condition, seems to have been peculiarly and benevolently designed by nature, when she made them, like fire, expansible over all space, without lessening their density in any point, and like the air in which we breathe, move, and have our physical being, incapable of confinement or exclusive appropriation. Inventions then cannot, in nature, be a subject of property.”

“Difference of opinion is advantageous in religion. The several sects perform the office of a Censor morum over each other. Is uniformity attainable? Millions of innocent men, women, and children, since the introduction of Christianity, have been burnt, tortured, fined, imprisoned; yet we have not advanced one inch towards uniformity. What has been the effect of coercion? To make one half the world fools, and the other half hypocrites. To support roguery and error all over the earth. Let us reflect that it is inhabited by a thousand millions of people. That these profess probably a thousand different systems of religion. That ours is but one of that thousand. That if there be but one right, and ours that one, we should wish to see the 999 wandering sects gathered into the fold of truth. But against such a majority we cannot effect this by force. Reason and persuasion are the only practicable instruments. To make way for these, free enquiry must be indulged; and how can we wish others to indulge it while we refuse it ourselves.”