The film provides some nods to the Wolverine limited series, where most of the characters are taken from:
- Instead of Harada, the film's Silver Samurai is old man Yashida. Since the comics name Kenuichio is not a real Japanese name, the film derives Yashida's name Ichirō from the actual Japanese name, Kenichirō.
- Mariko's arranged marriage, that she accepts as a thing of honor, which she does not expect Wolverine to understand because he's not Japanese.
- Ichirō pledges his katana to Logan as gratitude for saving his life. In the comics, Mariko is the one who pledged the Yashida katana to Logan after he kills Shingen.
- Like the film, the mini-series also took place shortly after Jean's death, and involved a love triangle with Mariko and Yukio.
- In the "Return of the King" arc of Ultimate X Men, Logan ends up running through a bear with his claws, although the film's version is much more peaceable and emotional.
- The Silver Samurai possesses the ability to heat up its blades, causing them to glow. This resembles the way the comic iteration of Silver Samurai coats his katana with a glowing tachyon field.
- In an example combined with Foreshadowing and Sequel Hook, a commercial for Trask Industries, the makers of the mutant-hunting Sentinels, can be seen at the end of the film.
- In the moments when Jean Grey is seen, it's in a white room. Perhaps representing Phoenix in the White Hot Room?
- The Alternate Ending has Yukio giving Logan a more realistic version of his classic yellow and brown and yellow costume from the comics. Complete with a mask!
- Mariko holding two of Wolverine's claws at the end could be an X-23 reference.
- Probably not intentional, but look at Logan's train-lunge. With the black trenchcoat, it's pretty reminiscent of Victor Creed's action scenes from X-Men Origins: Wolverine.
- In the comics' Fatal Attractions arc, Magneto stripped the adamantium from Wolverine's skeleton. In the movie, the Silver Samurai extracted Logan's Healing Factor from the marrows of his broken claws (removing the adamantium along with it.) Wolverine later regrows his claws, now in bone form.
- As he's known to do in both the comics and first X-Men movie, Logan hangs out with a young mutant woman.
