The picture of Miss Honey's father, Magnus, is actually a portrait of Roald Dahl, the author of the book "Matilda," upon which the film is based.
As a child, Miss Honey had a doll named Liccy Doll. One of the producers of the film is author Roald Dahl's widow, Liccy Dahl.
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.
At one point in the movie, Matilda's brother can be seen wearing a Napalm Death T-shirt.
Sadly, Mara Wilson's mother died of breast cancer during filming. Mara pressed on bravely, impressing her adult co-stars.
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.
Kylie Tyndall and Keaton Tyndall were originally cast as Young Matilda, but had to be replaced last minute due to high fevers and the flu.
The car Harry sells to the Trunchbull is a 1970 Buick Electra 225 sedan.
Pam Ferris would often stay in character when the director called cut in an attempt to actually scare the children on set so that their fear would be genuine when the camera was rolling.