Most people who have passed grade school are taught that men have one X and one Y chromosome while women have two X chromosomes. However, in Real Life it's not always that simple.
The whole issue of gender identity aside, anything that interferes with fetal development can cause various degrees of feminization or masculinization ranging from people who are genetically XY and physically female to people who are genetically XX and physically male to people who are intersex and whose anatomical sex is neither male nor female. There is also a phenomenon called chimerism which can cause different parts of the body to have different DNA, meaning DNA from someone's blood or saliva (the most common sources for DNA tests) may not match DNA from other parts of their bodies, which for fictional purposes usually means hair, skin or semen.
In fiction, this usually pops up in various kinds of detective stories and is used as an excuse to make a DNA test into a Red Herring. It can also be a source of drama or simply a character quirk. The actual cause is likely to be Hand Waved or just glossed over. Transgender people may fall under Wrong Genetic Sex if their transgender status is not known in advance and the plot hinges on the difference between their chromosomes and their appearance. Intersex people may also be included under similar circumstances. However, only individuals count: if an entire population is intersex, then it's a One-Gender Race.
See also Hermaphrodite, which may overlap but is in many cases a distinct phenomenon, and Intersex Tribulations. Both "hermaphrodite" and "pseudohermaphrodite" were used as medical terms for these conditions in the past but that usage was not strictly accurate and is now considered pejorative.
- In The Day of Revolution, the supposedly male protagonist discovers in the first chapter that he is intersex and genetically female. Despite some misgivings and with a push from her parents, she decides to reinvent herself as a girl.
- In Earth Maiden Arjuna, one of the female ecology activists has this as a result of medication her mother took while pregnant.
- IS: Otoko demo Onna demo Nai Sei is a manga about intersex people. It is originally a series of one-shots but later turns into a Coming of Age Story about one person named Haru.
- Kyoko, the protagonist of one of the arcs of Level E, is found to be one. Unfortunately, that might spell the end of Mankind (long story).
- Yoite from Nabari no Ou is revealed to be intersex in later chapters.
- The protagonist from —All You Zombies— starts out as an intersex female and... it gets complicated. Her actual degree of intersexualization approaches true hermaphrodism and wouldn't be biologically possible, except there's no logical reason why she'd be human anyway.
- Calliope (later Cal) from Middlesex was born intersex (genetically XY) and raised female until the age of fourteen. Notably, her being Raised as the Opposite Gender was completely unintentional on the part of both her doctors and her parents, since the doctor was nearsighted and had no idea that she was actually male. Cal also meets a woman with Complete androgen insensitivity syndrome, an intersex condition that causes the woman affected to be born with a vagina, but with XY chromosomes, no uterus, and internal testes where the ovaries would typically be. Despite being able to pass as a woman, she strongly identifies herself as a hermaphrodite and is an intersex rights activist.
- It's revealed that Graywytch from the Nemesis Series is intersex when she casts a spell to kill all humans with Y chromosomes (in her mind all men) and then collapses from her own spell. This came as just as much a surprise to her as the reader.
- A lot of the young adult novel None of the Above by by I.W. Gregorio deals with the teenage protagonist dealing with the realization that she has AIS.
- The Power: The Power draws a rather stark line between male and female. Jos's boyfriend Ryan is an example of how biology isn't quite so clear. Despite being overall male in biology, along with identifying as such, he has a chromosomal abnormality that means he also has a skein. In-universe, this is seen as an abnormality that is also grounds for having a particular fetish.
- The original incarnation of Sadako of The Ring was this, thanks to androgen insenstivity. In the book, she was thrown into the well by a doctor who had raped her, and then found out she was intersex.
- The big reveal in The Saga of Tuck is that the titular character's increasingly feminine appearance is due to 'his' being a chromosomal chimera, with both XX and XXY sets of chromosomes. Tuck was actually intersex at birth, though the doctors never told his family that they had 'corrected' this, a fact that made his mother furious when they learned the truth.
- It's implied in Wicked that Elphaba is intersex. In her case, though, she's still able to get pregnant and give birth to a son.
- A Season 8 episode Call the Midwife features a young woman, Lois, who is about to get married and is concerned that at the age of 22 she has never had a period. When she approaches the midwives about this, they refer her to a hospital where (after a very unpleasant and unfeeling examination by a doctor and a group of medical students) she discovers that she has "Testicular Feminisation Syndrome" (now called Androgen Insensitivity Syndrome). This causes her a massive identity crisis and leads her to break off her engagement and a suicide attempt. Thankfully, the Midwives and her mother are able to convince her that she still is the same person she always was and she and her fiance get back together with him telling her that he loves her regardless of the fact that she can't have children and of her condition.
- In one episode of CSI, a DNA sample with female chromosomes turns out to belong to a male character. He's a post-operation trans man, and it wasn't known that he's transgender.
- In Faking It, Lauren's plot revolves around taking some pills she's very defensive about. The rest of the main cast eventually finds out that she's intersex and androgen-insensitive.
- This is a major plot point in an episode of Freaks and Geeks when Ken's new girlfriend Amy tells her that she's one of these. There's no DNA test or anything — the conflict comes from Amy getting upset at Ken (who initially struggles with the revelation) telling his friends her big secret.
- In one episode of House, a woman turns out to be suffering from testicular cancer due to Androgen insensitivity syndrome. (In reality, androgen-insensitive women seldom have a significantly increased risk of testicular cancer; rather, the "threat" of cancer is used as an excuse to remove the gender-incongruous gonads despite their being fundamentally harmless.)
- One episode of Law & Order: Special Victims Unit starts with a rapist getting killed by his victim and the DNA evidence leads the detectives to a teenage boy who just happens to have an ironclad alibi. It turns out that his twin "sister" is actually his twin brother; it seems he lost his penis when they were circumcised as babies and the doctors who botched the operation covered their tracks by completing the job and talking his parents into raising him as a girl. Sadly, this is actually Truth in Television: The episode is based on an actual case. Just like the character in the episode, the real man vehemently reverted to a male gender identity as soon as he got the chance. Sadly, he ended up killing himself instead of killing the doctor like his fictional counterpart in SVU did.
- In Orphan Black, the genetic original person for both the female and male clone batches turns out to be the same person, an XX woman who had XY chromosomes in some of her cells due to chimerism.
- The Power (2023): Due to his intersex condition, Ryan (though he appears outwardly male and identifies as a man) also has the skein, while otherwise it's only developed in women or girls (who are cisgender). It is then revealed in "The Shape of Power" that trans women (implied for only those on hormone therapy) can develop a skein.
- In one episode of Whose Line Is It Anyway?, during a game of Party Quirks, Colin plays a character who suspects that people are not the gender they purport themselves to be and he spends his time during the game feeling up his fellow contestants.
- This comes up in Y: The Last Man (2021), as the phenomenon that killed almost all of the world's men seems to have specifically affected people with a Y chromosome. As a result, women who never knew they had a Y chromosome dropped dead on top of self-aware intersex people with one and trans women. The men other than Yorick who were spared, meanwhile, are in the reverse situation, though only trans men have been confirmed so far.
- The character Ramona in Sticky Dilly Buns is defined to be a fairly classic case of 17-beta-Hydroxysteroid dehydrogenase III deficiency, a condition similar to androgen insensitivity syndrome (see below under Real Life). She's a well-adjusted heterosexual woman; the fact mainly serves to bemuse some of the other characters.
- Chimerism has been found to be the cause of rare — sometimes seemingly impossible — coat colors in several species of animal, including dogs, cats, and horses. One particular horse appeared to be a stallion, but was found to have a blend of stallion and mare DNA; calico tomcats are the feline equivalent. Cross-sex chimerism can also occur in birds, although their mechanism of sex chromosomes is different (ZZ males vs ZW females). In fact, it's common enough that captive-breeders of parrots have a term ("half-sider") for a bird that displays one sex/color on one side and a different sex/color on the other.
- Human chimerism exists as well, but so far it has primarily been identified in women whose partners requested paternity testing of their children. The results showed that the father's DNA matched the children's but the mother's didn't. More extensive follow-up tests showed that the mothers' blood, skin or saliva (the most common mediums for DNA testing) had one DNA profile while her ovaries had another.
- In human beings and most types of animals all embryos begin with undifferentiated gonads connected to both ductus (vas) deferns and oviducts (Fallopian tubes). By default, the gonads will develop into ovaries and the vas deferens will disappear, but usually the presence of a Y chromosome causes an androgen reaction that makes the gonads instead become testes and the Fallopian tubes wither away whilst retaining the vas deferens. Complete androgen insensitivity syndrome is an intersex condition that causes the woman affected to be born with a vagina, but with XY chromosomes, no uterus, and internal testes where the ovaries would typically be. These women overwhelmingly identify as female and heterosexual.
- The "switch" for a fetus developing as a male is primarily controlled by just a single gene on the Y chromosome. The SRY gene is so crucial that a mutation on just this one gene can cause an XY female, and its translocation to an X chromosome can cause an XX male.
- XX male syndrome is a rare intersex condition that causes the male affected to have XX chromosomes, as well as small testes, varying degrees of gynecomastia, poor facial hair growth, and diminished libido. Men and boys with the condition are otherwise not particularly feminine.
- These cases tend to hit the news every Olympic year as various female athletes are accused of or found to be intersex even though no one has ever demonstrated these women actually derive any unfair advantage from this that exceeds those derived from other natural variations such as height, bone density or muscle mass. There is considerable evidence that most of these conditions actually make them immune to any boost XX females might get from male hormones.