There is a focus on sexuality throughout The Perks of Being a Wallflower, and this emphasis takes many forms. Charlie is fascinated by sex, and many of his letters detail how his sexual desires revolve around Sam. Ashamed of these yearnings, Charlie at first considers hiding them, but he eventually confesses to Sam how he feels about her. As his feelings grow, he also begins to talk about masturbation frequently - and about how he spends large portions of his day masturbating. The book's open discussion of sexuality has garnered criticism and is credited with the book's frequent placement among the top 10 most frequently challenged books, as determined by the American Library Association.
In addition to the discussion of Charlie's heterosexual sexuality, there is also an engagement with LGBTQ issues in Chbosky's novel. Even though Patrick is openly gay, he is forced to keep his sexual identity a secret in order to adhere to Brad's wishes. Brad's struggle to come to terms with his own identity is itself a moving account of a gay individual negotiating the harsh world of high school.
Finally, the theme of sexuality precipitates in the book's discussion of sexual abuse and molestation. Many of the characters have been molested in their pasts, including Aunt Helen and Charlie; this aspect of the theme indicates the cyclic nature of sexual abuse.