Contrary to the popular perception that his eyes were a different color, he actually had a condition called anisocoria.
Anisocoria is an unequal size in a person's pupils. David Bowie's left pupil was permanently dilated due to fisticuffs with a friend that resulted in his left eye being scratched and paralyzing the muscles that contract the iris. The permanent dilation meant that Bowie's left seemed to be much darker than his right eye. It also meant that he was more likely to experience "red eye" in photos.
Bowie harbored no ill will towards his friend for the unfortunate injury and in fact, expressed gratitude as the unnerving look of his eyes only added to his "mystique" and made him even more magnetic as a performer.*
