Most scholars agree that President Abraham Lincoln was a religious man. However, modern interpretations and newly discovered documents show doubt on the specific brand of Lincoln's religion, and how he practiced it in politics and his daily life.
One major issue with Lincoln's religion is that he refused to join a church. Naturally, since Lincoln is a beloved and highly respected figure in American history, many sects would be overjoyed to claim him as a follower. Normally, affiliation with a specific sect of Christianity would entail joining a church and attending its services, but Lincoln instead remained undeclared and seemed to prefer to keep his religious practices private.
Lincoln, according to his wife Mary, was:
A man, who never took the name of the Maker in vain, who always read his Bible diligently, who never failed to rely on God's promises & looked upon Him for protection, surely such a man as this, could not have been a disbeliever, or any other than what he was, a true Christian gentleman.
(Abraham Lincoln and religion, Wikipedia)
Obviously, the testimony of his wife came from a very close and intimate place, but could also be interpreted as those of a grieving widow who wished her husband to be seen as Christian.
Another issue is that of Lincoln's possible conversion from a non-believing position: various sources show clear statements on religious beliefs, while personal testimony -- such as those from his personal biographer, Colonel Lamon -- claim that he never used specifically religious speech or imagery in private, meaning that he did not personally believe in a higher power. His public speeches contained references to God: the Gettysburg Address included the line "this nation, under God, shall have a new birth of freedom," a reference not in the original draft.
Modern thought is more-or-less equally divided along two lines: that Lincoln was a deeply private man and so practiced his religion in private, not wishing his personal beliefs as President to affect the free practice of religion in the United States; or that Lincoln was a non-believer, ranging from agnostic to atheist, and so took pains to avoid specific and deliberate statements about God and religion.