There are two direct references to Hideo Kojima's previous game, Policenauts, in the game. In Hal's lab where the player first fights Gray Fox, there is a Policenauts poster on the northern wall. When talking to Otacon, he begins to express his love for Japanese animation and robots, showing footage from Policenauts as well.
In the Japanese version of the game, if the player has save data from Policenauts, Psycho Mantis will comment on it.