There are a few minor differences in the Genesis version of the game not present in the SNES Version:
•The title screen shows Woody with a devious face unlike in the SNES, where it shows him with an envious face.
•Upon clearing a level, Woody has a longer dancing animation.
•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 Nightmare Buzz boss fight was based on a scene deleted from the final film.