The tongue stud that Nikki Reed wore in the film was real, but Evan Rachel Wood's was not. It was made like a suction cup, but occasionally would fall off. Because of this, she ended up accidentally swallowing a few of them by the time the movie had finished filming.
During the belly piercing scene, Tracy says "What the fuck did you do" that was not scripted because Nikki Reed had actually poked the top of Evan Rachel Wood's belly with the needle. She still has the scar to prove it.
During a live Q&A on Ustream to celebrate the film's 10th anniversary, hosted by Reed and Wood, the actresses claimed that neither of them can watch the movie since they both have such strong emotional reactions to the film.
Throughout the film, there is a very prominent ad that shows a woman's white face, and underneath it are the words "Truth Is Beauty". The eyes of this woman belong to lead actress Nikki Reed. Throughout the movie, as Tracy falls deeper into trouble, the face becomes more distorted and dirty.
The director Catherine Hardwicke purposely changed the lighting through out the film to match the mood/distress of the characters. The further Tracy spiraled downward, the grittier and darker the lighting in the film became. By the end of the movie the color is almost completely washed out to black and white, as that is when Tracy finally reaches rock bottom.
The low-budget film was shot in an actual house that the crew had rented out for the duration of filming. Holly Hunter (Melanie) was amazed to see that the water worked. Brady Corbet (Mason) only lived about a block away from the house so he was able to walk to shooting.
Teenage singer/songwriter Katy Rose wrote the song "Lemon" especially for Thirteen (2003) after reading an article about the movie in the paper. "Lemon" is played during the credits, while another Katy song, "Overdrive" is in the film.
Evan Rachel Wood stated in the 10 year anniversary stream that for a while after the movie had wrapped, she'd find herself coming home from shopping and discover that she had, unintentionally bought very similar clothes to the ones they wore in the movie.
The language that Evie and Tracy speak in the kitchen the morning after Tracy's fight with her mom is a fake language called Gibberish. Tracy asks "why does my tongue hurt?" To which Evie responds "maybe because you give head."
The stars of this film Nikki Reed and Evan Rachel Wood would both go on to play vampires in future projects, Reed in the Twilight (2008) franchise as Rosalie, and Wood in True Blood (2008) as the Vampire Queen of Louisiana.
In the scene where Melanie questions Tracy about her belly button ring, a reference is made to rapper Bubba Sparxxx. One of Tracy's lines is taken from his first single, "Ugly" in which he raps, "That's just my mood now, I hate it came to this. How else can I say it? I don't speak no other languages."
Mara Wilson, most known for roles in Matilda and Mrs. Doubtfire, was sent this script to audition, but her father insisted she turn it down due to the films controversial storyline. She opens up about it briefly in her book: Where Am I Now? 
Evie refers to Brooke as three different things to her in the movie. First she refers to her as her guardian, then her aunt, and finally her cousin. Time codes for these different references are as follows: Guardian 00:18:12, Aunt 00:43:15, Cousin 00:43:36.
The trivia item below may give away important plot points.
The end scene where Tracy falls to the floor while crying and her mother Melanie is kissing her scars was so traumatic for Evan Rachel Wood that she blacked out and came to herself fifteen minutes later, being held and rocked by Catherine Hardwicke, the director of the movie.