In the making of segment on the DVD, Danny DeVito reveals that for the chalk to write by itself, they wrote the letters backwards on the opposite side of the chalkboard, then put a magnet on the chalk. They then had someone stand behind the chalkboard and write the words backwards with a device that attracted magnets.
Matilda, when describing her love of Charles Dickens to Miss Honey, accidentally mispronounces his name as "Dahl's Chickens." This is a nod to another novel by Roald Dahl, "The BFG," in which the title character continuously mispronounces Charles Dickens' name.
Near the end of the film, Matilda tells Miss Honey about the speed of a mouse's beating heart. This is a subtle reference to another book by Roald Dahl, The Witches, in which the protagonist and his grandmother have the same discussion.
Feature film debut of Craig Lamar Taylor. He went on later to play Malcolm's wheel-chair bound, slow talking, best friend on the television series Malcolm in the Middle. He plays the little boy who catches the newt which falls off of the light fixture - after The Tunchbull's "dance" caused by Matilda using her powers to tip the glass from which Trunchbull drinks.
The credits on the DVD version list the Newt as played by Mr. Speaker, Sir Isaac, and Wayne. This is a reference to: Newt Gingrich, the Speaker of the US House of Representatives; Sir Isaac Newton, English physicist; and Wayne Newton, the singer.
This film features no less than three actors from the Tim Burton Batman films: Danny DeVito, who directs and co-stars, played the Penguin, also known as Oswald Cobblepot, in Batman Returns (1992). Paul Reubens, who plays one of the FBI agents hunting Harry Wormwood, also appeared in Batman Returns as the Penguin's father. Tracey Walter, who plays the other FBI agent, played Bob the Goon in the original Batman (1989).
One of the lunchboxes reads, "Greeting from Asbury Park, New Jersey", a reference to Danny DeVito's hometown. "Greetings from Asbury Park, New Jersey" is also the name of Bruce Springsteen's first album.
Several times in the film, the word "twit" is used by Harry Wormwood and Ms. Trunchbull. This could be a reference to a book called "The Twits" by Roald Dahl who wrote the book this movie is based upon.
Mara Wilson had been a fan of the book ever since the age of four, when she had overheard her mother reading it to other children. After the success of Miracle on 34th Street, Matilda was among many scripts she was offered. She chose it immediately.
It's widely believed that the Trunchbull was based off the headmistress of Liccy Dahl (who served as a producer) - who reportedly got very creative with her punishments. Liccy and her friend once tried to sneak ice cream to their rooms. When they were caught,the headmistress made them wait until dawn while the ice cream melted.
Mara Wilson's mother died during production of the film. She had thought for years that her mother had never gotten to see the completed film. But years later, Danny DeVito revealed he had shown her a rough cut of what they had filmed shortly before she died.