Was strongly inspired by the director's personal memories, especially his relationship with his uncle, who supposedly came back as a ghost.
The Spanish comic series "Paracuellos" by Carlos Giménez was an important source of inspiration. This semi-biographical work takes place in a Francoist orphanage during the early 50's. Giménez worked as a storyboard artist on this film.
Guillermo del Toro has said that this is his favorite movie of his own (2003).
This labor of love for director Guillermo del Toro was sixteen years in development.
The film came together when Guillermo del Toro bumped into Pedro Almodóvar at the 1994 Miami Film Festival where he had just shown Cronos (1993). Almodovar told him that he had just seen his film and wanted to produce his next movie.
The design of the ghost was inspired by the white-faced spirits of Japanese horror films like Ringu (1998).
The film's title refers to the medical condition of spina bifida.
Described by Guillermo del Toro as being a sibling film to Laberinto del fauno, El (2006) (this being the masculine "brother" film, and Pan's as the feminine "sister" film).
The character of Jaime is heavily inspired by the famous Spanish comic writer Carlos Giménez.