Yes.
- In the comic books, Ducard and Ra's al Ghul are two separate beings. Unlike the comic incarnation, there is no direct indication that al Ghul has any supernatural powers. He also ran the League of Assassins in the comics, whereas he leads the League of Shadows in the film. Also, his ultimate goal is to rid the world of injustice in the film, rather than saving the environment in the comics.
- When Batman first started fighting crime, Jim Gordon was already Lieutenant. Instead, he is Sergeant. He is, however, promoted to Lieutenant in the end of the film.
- Flass, while having a similar characterization, is physically the opposite of his comic doppelganger, who is tall, well-built, and blonde.
- Harvey Dent was the Gotham D.A. when Batman started fighting crime in the comics. Instead, Finch is the D.A.
- Batman never met Ra's al Ghul during his years before Batman, and did not train under him. He did train under Ducard, though.
- Commissioner Loeb is a portly, old white man and corrupt in the comics, but in Batman Begins, is a tall African-American, with no indications that he's corrupt.
- Gordon, in the comics, transferred to Gotham from Chicago shortly before Batman appeared. Gordon in Batman Begins has been with the Gotham City Police Department since Bruce was a child.
- Rachel Dawes is a character created for the film, and has no doppelganger in the comics.
- Joe Chill had no encounters with Carmine Falcone in the comics.
- Bruce's parents were killed in Crime Alley in the comics, while in Begins, they are killed outside an opera house. Also, in the comics, they were killed after seeing a Zorro picture, while in Begins, they are seeing an opera.
- Gordon and Batman become allies much faster in Begins. In the comics, their alliance wasn't formed for a while after Batman appeared.