Both versions share similarities with Nintendo's Metroid franchise, as Wolverine jumps and attacks through large multi-floored levels, attacking doors to give him access to new areas. It's also here were both versions have some major differences as well. The SNES version requires a set amount of enemies to be destroyed before entry to the next area is granted. The Genesis version however, has a countdown timer that expires if the player takes too long, where upon the Wolverine comic character Elsie-Dee automatically finds Wolverine and kills him, wasting one of his 5 lives. Both games give Wolverine a percentage of his available health, always starting at 100%. Upon taking damage, his energy will recover overtime thanks to his mutant healing factor. The SNES version has this being a slower process, but the player can wait as long as they want to regain 100% health. Genesis users however don't have that luxury as the previously mentioned count down timer will keep them moving.
Wolverine also has different move sets based on what version the game is being played on. The SNES for example, has Wolverine being able to climb on any wall or ceiling with his claws, and is able to make springing leaps. The Genesis version has Wolverine being able to roll up into a ball and travel short distances, much like the Metroid heroine, Samus Aran.
Each stage is usually ended with a boss confrontation, and these differ from level to level between each version as well. The Genesis game also places more emphasis on basic puzzle solving, and not level navigation and enemy destruction like the SNES version does.