Since its original publication in 2007, The Absolutely True Diary of a Part-Time Indian has appeared several times on the list of the top ten most challenged books put out by the American Library Association. The book is usually challenged because of its use of profanity, violent moments, and references to sex, with parents believing none of this is appropriate for their children when it is assigned to them in a classroom setting.
The protagonist, Junior, uses profanity on occasion in the book, as do other characters (for example, Junior calls his bullies "assholes," and his bullies on the reservation call him a "retard" for his physical disabilities). Sexual themes are present in the book as well, though they are not the main focus. The most explicit reference to sexual themes in the book occurs when Junior discusses masturbation and how he is not ashamed of it nor does he believe it is a sin.
Some parents have objected to the book's themes regarding violence and alcoholism. Junior's friend Rowdy has a bad home life with a father who regularly beats him and his mother, and several people Junior knows on the reservation suffer from alcohol addiction. These themes, while realistic, are seen as too mature for high-school readers, leading to the book being pulled from certain school libraries and reading lists.