Big Boss & Solid Snake are father and son. While their Japanese voice actors Chikao Ôtsuka & Akio Ôtsuka are father and son in real life.
In an original draft of this game, the ending had Solid Snake and Otacon turning themselves in for the crimes they committed, and executed. Most of the staff vetoed this option, so it was not used.
Unlike regular PMC troops, the all-female Haven troops cannot be knocked unconscious by grabbing their crotch after a body search (it turns into a grope). If Snake attempts this, the soldier will yell "Pervert!" "You idiot!" or "You men are all the same!" and retaliate with an incapacitating kick. However, if wearing the Young Snake FaceCamo, they seem to enjoy the action.
During development of the game, Hideo Kojima wanted the Beauty and the Beast Unit to be naked, though this would have severely affected the game's censorship rating. Yoji Shinkawa stated that the motion capture actors were asked to do the motion capture nude, though this could also not be used in the game.
PS3 Trophy achievements were not added to this game until four years after it was released.