The film was originally conceived as a R rated picture and was shot with that rating in mind. However, following the success of other PG-13 rated horror movies like The Ring (2002), executives at New Line asked the director to tone down the violence and language for the more commercial lower rating. This was done by shortening the demise of Frank Martin and cutting some of his profane dialogue.
The film makers suggested making Willard a very rat-like human and requested the make-up artists make Crispin Glover unattractive and nervous looking by accenting the hard angles of his face, making him pale, dark around the eyes, and making his distinct nose stand out.
There have been reports that the enormous rat Ben was not portrayed by a rat, which is not quite true. Ben was played by a giant Gambian Pouched Rat (cricetomys gambianus), a distant relative of the Norway rat (rattus norvegicus), the species in the film. Gambian pouched rats, while fairly docile, can grow to body lengths of as much as 10-17 inches from head to base of tail, with a tail about the same length again or longer, and generally weigh anywhere from two to over six pounds.
The part of Cathryn was written for director Glen Morgan's wife Kristen Cloke. Cloke got pregnant and had to withdraw. She played a small role as a psychiatrist, though. That scene was cut during post-production, but can be seen on the DVD-release.
Willard's mother tells him she should have given him a better name. The meaning of Willard is "Will Brave", the opposite of Willard's skittish demeanor. The name she tries to give him, Clark (i.e. Clerk) is Willard's occupation at Martin-Stiles.