Lincoln wrote to his life long friend, Judge J.A. Wakefield, this “testament” of his beliefs:
“My earlier views of the unsoundness of the Christian scheme of salvation and the human origin of the Scriptures, have become clearer, and stronger, with advancing years, and I see no reason for thinking I shall ever change them.”
Lincoln’s law partner, William Herndon, in the years following the assassination, said:
“Mr. Lincoln was an infidel, sometimes bordering on atheism.” “He never mentioned the name of Jesus, except to scorn and detest the idea of a miraculous conception.” “He did write a little work on infidelity in 1835-6, and never recanted. He was an out-and-out infidel, and about that there is no mistake.”
When Lincoln was asked why he includes God stuff in some of his speeches “Oh, that, is some of Seward’s (Secretary of State) nonsense, and it pleases the fools.”
“When Dr. Holland asked Mr. Herndon about his partner’s religious convictions, Mr. Herndon replied that he had none, and the less he said on that subject the better. ‘Oh well,’ replied Dr. Holland, ‘I’ll fix that.’”
— Franklin Steiner, The Religious Beliefs of Our Presidents, p. 112, on Dr. Josiah G. Holland, later editor of Scribner’s Monthly, having spent only two weeks interviewing Lincoln’s friends before preparing his Biography, in which Holland fabricated accounts of Lincoln’s piety
“No one of Lincoln’s old acquaintances in this city ever heard of his conversion to Christianity by Dr. Smith or anyone else. It was never suggested nor thought of here until after his death…. I never saw him read a second of time in Dr. Smith’s book on Infidelity. He threw at down upon our table — spit upon it as it were — and never opened it to my knowledge.”
— William Herndon, quoted in Franklin Steiner, The Religious Beliefs of Our
Presidents, p. 124
Found in a comment at about.com by a poster identified as "Freethinker" and corrected for spelling. A balanced evaluation of the matter can be found at Wikipedia.
The claim that Lincoln was an atheist seems unlikely, but that notion that he identified as a Christian for any substantial portion of his adult life seems doubtful as well.