Viktor Krasnov, 38, made the remark as well as others on a local website in his southern hometown of Stavropol.
A local complained, accusing him of "offending the sentiments of Orthodox believers", and he was charged under Russia's blasphemy laws introduced in 2013.
Mr Krasnov was sectioned in a mental institution for a month before being deemed fit to stand trial, and appeared in court on Wednesday.
His lawyer has said he is "simply an atheist", and that he was not just targeting Christians with his comments.
Human rights organisations have criticised Russia's blasphemy laws saying they limit freedom of speech, but the Russian government says there are to protect minorities and prevent religious violence.
