This article is from the X-Men Comic Books FAQ, by Kate the Short (firstname.lastname@example.org) with numerous contributions by others.
There are many, many ways that the movie is different from the actual
mainstream continuity of the comics. For one, the school has far more
mutants in it than the casts of Uncanny, X-Men, Generation X, and the
Hellions/New Mutants/X-Force kids combined.
The team in XM:TM consists of Cyclops, Jean Grey, and Storm, all led
by Xavier. In movie continuity, Cyke and Jean are not yet married
(though they share a room in the mansion), and Jean is a doctor.
Wolverine and Rogue first meet in Canada, instead of meeting when Rogue
runs away from the Brotherhood of Evil Mutants and comes knocking at
Xavier's door. A few other things must be noted about Rogue. First of
all, in the regular comics Rogue has the powers of flight and
invulnerability, which she gained from Ms. Marvel in the classic
Avengers Annual #10. She's also had her distinctive white stripe from
the get-go. Furthermore, the Rogue of the comics has *never* revealed
her real name on-panel, and it's strongly believed that if anyone knows
it other than Rogue's original parents, it would be Mystique (Rogue's
foster mother) or Destiny (Mystique's long-time companion).
The villains and supporting cast also have changed. Toad probably
received the most changes to his character, and all are improvements.
The Toad of the comics was always an Igor-like hunchback to Magneto, and
usually did little more than jump around uttering annoying lines. The
Toad of XM:TM, however, can climb walls much more efficiently, has a
strong tongue that can grasp items, and a rather nasty ooze.