"Intersex" is a term that refers to variations in sex characteristics including chromosomes, gonads, sex hormones, or genitals that don't fit the standard binary definition of "male" or "female". It most commonly refers to individuals with ambiguous genitalia. However, in a medical context, it can also refer to conditions such as androgen insensitivity syndrome, XX male syndrome, and certain hormonal disorders like polycystic ovarian syndrome.
Intersex characters are frequently depicted as androgynous, either in a Dude Looks Like a Lady, Lady Looks Like a Dude, Pretty Boy, Bishōnen, or Bifauxnen manner. They are frequently uncomfortable about their bodies in a manner similar to gender dysphoria. Their intersex status often leads to a lot of internalized angst or angst that can be brought upon them by others. Intersex characters are also frequently depicted as villains, leading to Unfortunate Implications.
Historically, intersex people have been referred to as hermaphrodites, however the two are not the same and it is considered offensive to refer to intersex individuals as such. Some intersex people identify as transgender, especially if they're non-binary or if they were raised as one gender growing up but don't identify with it; however, not all intersex people are trans. Despite this, being intersex is often pinned under the LGBTQ umbrella, in part because they often face the same (or very similar) forms of discrimination, bigotry, and ignorance.
- The Bishōnen Yoite from Nabari no Ou is revealed to be intersex late into the manga. It isn't given much detail but it is used to explain his angsty personality and identity issues more in-depth. His own parents thought that being intersex was a sign that he was cursed.
- IS: Otoko demo Onna demo Nai Sei is a manga about intersex people. The first two volumes are one-shots about various individuals, such as the female-identified Ryoma, who was raised male and ended up having her first period in her late teens. After volume 3, it becomes a Coming-of-Age Story and Queer Romance story about an intersex boy named Haru.
- Megumi from The Day of Revolution is intersex, but was raised as a boy named "Kei". Upon learning about Megumi's chromosomes, it's decided that she should transition into living as a girl. Megumi originally hates the idea but comes to accept it.
- Apos, the Big Bad of Mnemosyne is intersex (self-identifies as male), which in that universe is very handy as it gives him Immortality (a female-only ability) as well as the powers of an Angel (male-only ability) upon ingesting a Time Spore. Though it does come with Great Insanity and an unnatural pleasure from prolonged torture of his victims.
- Requiem of the Rose King is a loose adaptation of William Shakespeare's Henry IV and Richard III in which rather than being a hunchback, Richard's "deformity" is being intersex. His mother calls him a "demon" and claims he's cursed.
- Ghost Talkers Daydream: Haru is revealed to be one, as part of her backstory in chapter 12. It lead to her being bullied at school and eventually caused problems in her relationship with Inspector Gada. All of which caused her to develop a deep-seeded hatred for other women, due to her own sexual inadequacy.
- Little Fires is a Warriors fanfic about a transgender tortoiseshell she-cat. It is heavily implied that, like most tortie toms, Emberpaw is intersex. The Clans don't fully understand the condition but they do know that tortoiseshell toms are both very rare and oftentimes sickly. Emberpaw herself was weak as a young kit. She also doesn't enjoy living as a boy, but others don't understand her dysphoria and make fun of her femininity.
- The live-action film Spork is about an intersex, female-identifying elementary school child. It follows her figuring out her identity and relationships with other characters.
- The Wicked Years: It's implied in Wicked that Elphaba is intersex. At birth, her sex is difficult to understand until she's fully cleaned. Later in life she's noted as being lanky and androgynous looking. Elphaba displays discomfort with her body and won't even let her lover Fiyero touch her below the waist. Fiyero also notes that Elphaba has an unexplained scar near her groin, which may be due to an intersex-related surgery. In her case, though, Elphaba's still able to get pregnant and give birth to a son, Liir.
- In None of the Above by I. W. Gregorio, champion hurdler and homecoming queen Kirsten Lattimer finds her life turned upside-down when she's diagnosed with androgen insensitivity syndrome.
- Sadako from The Ring was born with androgen insensitivity syndrome and was killed because of it. She's later reborn as a "complete hermaphrodite".
- Annabel by Kathleen Winter is a 2010 novel about an intersex individual born in 1960s Canada. They were born with a penis and vagina, but their father decided to raise them as a boy named "Wayne". As Wayne grows, they show feminine traits that their father disagrees with. Upon hitting puberty, Wayne gets their period and is put on testosterone, which causes more confusion. The novel ends with Wayne discontinuing their medicine because they wish to be more feminine. Annabel has been met with praise, however intersex rights organizations found it flawed and inaccurate.
- Abigail Tarttelin's novel Golden Boy is a Coming-of-Age Story about Max Walker. He's a "golden boy": attractive, athletic, intelligent, and from a well-to-do family. However, his family keeps it a secret that Max is intersex.
- In A Dance with Dragons, fifth book of the A Song of Ice and Fire saga, George R. R. Martin introduces "Sweets", the purple-haired violet-eyed intersex prized slave of Yunkish slaver Yezzan zo Qaggaz, who owns a grotesquerie of unique and deformed slaves. Though Sweet's place of origin is unknown, the books do reference that people born in the cities close to the devastated Valyrian peninsula are often born with deformities and alterations.
- Nemesis Series: The transphobic Greywych casts a spell to kill off "men" (by her definition, anyone with a Y chromosome) but almost dies when she casts the spell. Danny theorizes that it's because she's likely has a Y chromosome and androgen insensitivity, though Greywych insists that it's just because of the spell is so powerful she accidentally Cast From Hitpoints.
- In the later Time Scout books, Dr. John Lachley was born with ambiguous genitalia. A little of each. Combined with a terrible childhood in the Crapsack World of Victorian London's East End, and you've got one hell of a Freudian Excuse.
- Elise Kavanaugh from The Descent Series is the only female on record to be a kopis (demon-slayer and exorcist), which appears to be tied to the fact that (as revealed in book two when she visits a gynecologist in a flashback) she's intersex: she has an XY chromosome pair and an androgen insensitivity disorder. It's a touchy subject for her, as her boyfriend Anthony finds out the hard way.
- In Night and Day, Alex Wells and Roxanne Doyle's baby, Alex Jr, is born intersex, leading to a disagreement between the couple over whether to subject the baby to an operation. An adult intersex character, Patrice, is also briefly featured as part of the storyline, when Roxanne attends an intersex support group.
- Stuart "Magilla", the first friend Delia makes in Everwood was born intersex and his parents chose to raise him as a boy. This poses problems when Stuart is caught playing dress-up with Delia and his parents freak out, forbidding Delia to play with their son and hastily switching him to an all-boys school. Stuart's parents are the first and possibly only people in the series Andy is unable to help or reason with.
- The Farscape episode "Fractures" features Moya's crew making the acquaintance of another gang of fugitives escaped from Peacekeeper custody. One of them, a Nebari named Hubero, turns out to be intersex: effectively exiled from her people, she bitterly refers to herself as "not exactly male, not exactly female, not exactly anything." As it turns out, intersex individuals - known as "androgen" — are a persecuted minority in the highly-conformist Nebari culture, to the point that most are executed at birth; Hubero only managed to avoid this because she grew up on an isolated liberal colony, but when the Peacekeepers raided it and tried to ransom her back to her people, Nebari Prime refused to take her in. Needless to say, she's the most guarded of all the fugitives, and only feels comfortable revealing herself to Chiana — another Nebari exile and cultural rebel.
- Issue 9 of The Secret World introduces Kaoru, a character heavily implied to be intersex. Among other things, she was mercilessly bullied after being seen swimming in public and attempted to drown herself as a result; following the breakdown of her relationship with Ricky Pagan, she believes that it was prompted by him seeing "the real me"; finally, Ricky himself claims that he didn't dump her because of "what was between her legs" and insists that "everyone's bits are beautiful!" It turns out that he actually dumped her because of a tattoo on her thigh indicating that she works for the Phoenician Brotherhood; despite their shady status, Kaoru believes that they're the only faction in the Secret World that will accept her.
- In The House in Fata Morgana, Michel is believed to be female at birth, but he suffers from gender dysphoria from a young age and eventually realises he's a man when his body becomes more masculine and much more comfortable to him at puberty. Since he was born in The Middle Ages, however, his apparently supernatural transformation causes his family to consider him cursed or demonic, and this combined with his albinism and insistence on being accepted as a man despite lacking a penis lead to his imprisonment and torture in his family home. Even after escaping to the titular house and eventually falling in love, he calls himself cursed and doesn't dare to tell his girlfriend the truth or get intimate with her, as his worst fear is that she'll reject him and say that he isn't really a man due to his anatomy.