First game since Mega Man X2 on the SNES in which Zero is not immediately playable.
When the game was first released overseas. There was Japanese voice acting. But when the game was re-released in Megaman X Collection, the Japanese VA was removed, even the names of the voices were removed from the credits.
Because of the poor English translation most of the game received many people believed, incorrectly, that Sigma's dialog near the end was also a result of poor translation. The game itself points out that it is due to Sigma being in an unfinished state, Sigma has messy dialog in the Japanese version too.
The captive reploids in Blizzard Wolfang's stage share names with many well-known Capcom characters:
- Ryu, Ken, Chun (Chun Li): Street Fighter II: The World Warrior (1991).
- Guy, Cody: Final Fight (1989).
- Moringa (Morrigan): Vampire: The Night Warriors (1994).
- Leon: Resident Evil (1996).
- Arthur: Ghosts 'n Goblins (1985).
- Data: Rokkuman DASH (1997).
- Nina: Breath of Fire (1993).
- Batsu: Shiritsu Justice gakuen (1998).
- Regina: Dino Crisis (1999).
- Dante: Devil May Cry (2001).
- Gomez: "El Dorado Gate".
Final X series game for the Playstation 1.