This is what the wiki says:
"Kirito's avatar in GGO is the rare «M9000» type, which is speculated to be the result of an extremely rare occurrence of the system misinterpreting the player's brain waves (the system identifies the gender of the player via their brainwaves, but, on rare occasions, due to some impulse, it chooses the appearance of the opposite gender). It is an avatar that many male players dream of having, due to its female appearance. He retains his black hair, which now flows down to his shoulders. He has a pale skin and crimson lips, and shining black eyes, fringed by long eyelashes. If one did not know better, it would be easy to confuse him with a female. This often causes great confusion to people, such as Sinon."
Did this not happen in SAO? You know, that girl and guy that turned out to be two guys when given the mirror?