Director Catherine Hardwicke has called Nikki Reed a "surrogate daughter", having known her since she was 5 years old. The two began the screenplay as a comedy project which would be shot to video at minimal cost. The screenplay was written in 6 days and quickly shifted into a tale of early teen angst and self-destruction in Los Angeles, with Tracy's character drawn from Reed's own recent experiences as a pre and early teen. Hardwicke didn't think it would be fitting for Reed to play Tracy and auditioned hundreds of girls for the part.

After becoming aware of Evan Rachel Wood, Hardwicke came to believe she could make the film only with Wood in the role of Tracy and only that year, with Wood at that age.

Hardwicke has said Holly Hunter's agreement to play the role of Tracy's mother Melanie was a key boost to bringing the production together. About $2,000,000 was then raised, almost all through independent equity financing, a very low budget for any American film meant for general cinematic release in the early 21st century. Most of the adult actors were widely known and all of them reportedly agreed to low pay because they liked the script along with other members of the cast and crew. Wood and Reed were both 14 during filming (Wood turned 15 during the shoot). Most of the film was shot in August 2002 in Los Angeles, California.

Their first audition together was at Hardwicke's house, which wound up as a slumber party that night. Auditions took place on a bed in Catherine Hardwicke's house, and when Hardwicke auditioned Wood, she had her get into her bed with Nikki Reed. The wardrobe worn by the girls was mostly their own. As filming progressed, the girls began dressing similarly without being asked to do so. The girls did not take any dangerous substances during the film. They are shown smoking cigarettes, but these were filled mostly with catnip. The crushed pills they are shown snorting from the cover of a children's book were harmless dietary supplements.

All of the scenes in which Tracy cut herself were shot in a single day; Wood recalled running to her brother for emotional support between some takes. Wood later described the shooting of the two make out scenes with Javi and Luke as "awkward" because her family was watching behind the scenes. Wood's mom requested that in the scenes with Tracy's bra exposed, that the front of her not be seen on camera. The whole scene with Luke was rendered in a single, long and uncut take with Wood, Reed and Pardue, but was tightly choreographed with several crew members, social workers and parents also in the small room, carefully staying either hidden or behind the camera as it panned more than 200°, showing all four walls.

The movie was shot on lower-cost super 16mm film. The camera was small, had a Panavision lens and was mostly hand-held by cinematographer Elliot Davis. This allowed shooting in very tight spots, such as in the bathroom. One tracking scene was shot with the camera mounted on a discarded shopping cart, which the crew happened to find nearby.

Most of the scenes were filmed on location, with some on Melrose Avenue, Hollywood Boulevard, Venice Beach. The Freeland home scenes were shot at a rented house in the San Fernando Valley. The many outdoor school scenes were shot at Portola Middle School in Tarzana, most of them on a single Saturday in searing heat. Many of the extras were students and a few were crew members.

Some scenes in the film were carefully and colorfully lit, while others were shot only with whatever daylight could be had. The shooting schedule was limited to less than a month. The underage actors could work only five-and-a-half hours each day, closely watched by a paid social worker.

This made for a frenetic production atmosphere, which cast and crew later said matched the script and added to the film's fast and emotionally taut pace. The film stock was transferred to the digital domain wherein the colors and saturation were highly manipulated for some segments. The beginning of the film was very slightly desaturated in the scenes before Tracy became friends with Evie. Once they became friends, the saturation was increased to a "glowy" effect, according to Hardwicke. After the scene where Evie and Tracy make out with Luke, the saturation slowly becomes less and less until the end of the film, especially after Evie is told that she can't live with Tracy anymore and Tracy is abandoned by the popular group.

Thirteen was picked up by a major distributor only after production was completed. Because of the film's R rating in North America, the underage stars had to be accompanied by adults to see it at public showings. Reed stated in 2012 that she regrets the way she portrayed her family in the autobiographical film, saying, "I wrote this movie about them and their flaws and imperfections and what it was like growing up. It was from one kid's perspective and not a well rounded one. You get older and it's like, how dare I portray my father as being a totally vacant careless schmuck?"

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