Trivia: The smile that Damien gives at the very end wasn't scripted. Originally, Damien was supposed to "look really mean," but Harvey Stephens couldn't keep a straight face: he started to smile, then laugh. Richard Donner decided that the smile made Damien look even more evil, so it stayed in the movie.
Trivia: Richard Donner was originally wary of sending the script to Gregory Peck. Combined with the original ending, in which Robert kills Damien, and the fact that Peck's son had recently committed suicide, Donner thought offering the film to him was distasteful. But to Donner's surprise, Peck agreed relatively quickly to do the film.
Answer: It's possible that the mark didn't appear until Mrs Baylock showed up and began teaching him about his heritage. The mark of the devil is said to appear only when Satan accepts a follower, and up until Mrs Baylock appears, Damien is a normal boy. Yes, he's the devil's son, but he knows nothing of his evil nature until she starts teaching him. In fact, at one point, Robert mentions that he knew every inch of Damien's body since he raised him and never saw anything, so more than likely the mark didn't appear until Damien had areas on his body where it could be hidden more easily.
dewinela
But it's a birthmark. He had it when he was born.