There are a number of differences between the Genesis and SNES versions of the game:
•Woody's expression shown in the title screen is different between the two versions.
•Upon clearing a level in the Genesis version, Woody has a longer dancing animation.
•Cutscenes in the Genesis version have more still images from the movie than the SNES version.
•A bonus game can be played in the Genesis version if you collect a certain number of stars, which is omitted in the SNES version.
•The Day-Toy-Na level bears a striking resemblance to Outrun, which was also released for the Genesis. However, it is not present in the SNES version of the game.
•The staff credits in the Genesis version showcases the character models that were present in the game, which is ommitted in the SNES version.

The Nightmare Buzz boss fight was based on a scene deleted from the final film.