- In the book, there are scenes that show Stanley at school the day he was arrested. These are not in the film, but in the deleted scenes.
- Stanley in the book is fat, but in the movie, he is skinny. However, a woman who worked on the movie explained in a special feature that this was because his weight would have to change constantly since the shooting schedule was all over the place.
- In the book, Stanley's father wants to find a way to recycle sneakers, and he accidently created the Sploosh, but in the film, he only experiments with how to get rid of foot odor.
- In the film, the roles of Mr. Sir and Mr. Pendanski slightly swap: Mr. Sir is the one who saves Stanley after he digs his first hole and expresses his concern when Stanley runs away.
- In the film, the contents of the chest are much higher than the book.
- In the book, Sam and Kate kiss in the rain outside the school and are spotted by Hattie Parker as she leaves a store. In the film, they are spotted kissing in the school house by Trout as he rides by the window on his horse.
- In the book, Zigzag accidently hits Stanley in the back of the head with a shovel. In a deleted scene, Squid does this.
- In the book, Armpit is stabbed in the stomache by the Warden with her pitchfork for going to the bathroom too much. In a deleted scene, it is Magnet who is stabbed.
- The film more dramatically depicits the huge hole, showing a network of tunnels. The book simply says that three holes came together until it was one.
- In the book, Elya Yelnats is 15, but in the film, he appears to be in his late 20's or early 30's.
- In the book, it is said that Elya was a friend of Madame Zeroni, but this isn't stated in the movie.
- Mrs. Morgeno's car in the book is a BMW, but in the film, it is a Jaguar.