A novel by Jeffrey Eugenides published in 2002 which went on to win the Pulitzer Prize for Fiction.

Calliope (later Cal) Stephanides was born with a rare genetic condition that caused her to look externally female, but in adolescence begin developing male characteristics.

That's not really the point, though. Most of the book recounts the story of Cal's parents and grandparents who happened to make such a trait possible.

A very well-written book, although it comes with a few warnings: much of the plot focuses on Brother-Sister Incest, and one character turns out to be a historical figure, Wallace Fard Muhammad.

This book contains examples of:

A-Cup Angst: One of Calliope's big concerns while she still thought she was a girl. See Pettanko below.
The Beard: Jimmy Zizmo is this for Lina, who is a lesbian and had to leave Bithynios after her affair with another woman was discovered.
Blind Mistake: The fact that the doctor who delivered Callie was nearsighted and didn't notice her unusual genitalia had huge effects on the lives of everyone involved, especially Callie.
Body Horror: The realization that Calliope's body is not normal has aspects of this.
Brother-Sister Incest: Desdemona and Lefty.
Closet Key: "The Obscure Object" for Cal
Elegant Classical Musician: Milton's clarinet skills are initially what make him attractive to Tessie. They even use it in foreplay.
Faking the Dead: Jimmy Zizmo
Generational Saga
Get On With It Already: The first half of the book that recounts Desdemona, Lefty and their children's lives can feel like this.
Groin Attack: Played for drama. Certain forms of physical activity proved to be excruciatingly painful for Callie's undescended testes back when she wasn't aware of having them.
Important Haircut: One of the first things Calliope does to change to Cal is get a short haircut.
Incest Is Relative
Intersex
Kissing Cousins: Tessie and Milt - though they didn't know that they were actually much closer than that.
Large Ham: Cal's narration borders on this at times. Justified in that when it does, he's lampshading Greek epics, which have the tendency to do this.
Married At Sea: Desdemona and Lefty, and the fact that their documents were conveniently lost in sacking of their home town made it possible.
Merlin Sickness: Lefty develops a purely psychological version of this after his second stroke.
Motor City: The book is set in Detroit and its tonier suburbs, and events in that city repeatedly interplay into the lives of the Stephanides family. Notable examples include Lefty's ill-fated job on the assembly line at Ford, bootlegging across the Detroit River to Windsor during Prohibition, the founding of the Nation of Islam, and the 1967 riots and the fallout thereof.
Nobody Over 50 Is Gay: Averted by Lina, who only came out after she was over 50. Of course, the rest of the family knew well before then:
Cal: Lina was, as Aunt Zo put it, "one of those ladies they named the island after."
No Periods, Period: Averted in that periods are discussed, but since Calliope doesn't have a uterus she can't actually get them and fakes them so her mother won't suspect anything.
Only Known by Their Nickname: The Obscure Object, and Cal's brother Chapter 11 (referencing how he went bankrupt later in life).
Pettanko: Calliope was initially thought to be this until the truth about her body was discovered.
Pass Fail: It's somewhat complicated, but Jimmy Zizmo, Cal's maternal grandfather, made himself the persona of Wallace Fard Muhammad (a real person who founded the Nation of Islam) after faking his death. Additionally, the way his origins are discussed by the characters and the narration, Zizmo could genuinely be of mixed ancestry and passed as Greek, Turkish, and Polish before faking his death and assuming his new identity; or he could genuinely be Greek, Turkish, and Polish, and be passing as a mulatto. The novel is delightfully ambiguous on this.
Pronoun Trouble: Cal runs into a bit of this, and even trying to talk about them in this article is a bit awkward.
- Which is precisely why Eugenides wrote the novel in first person.
Raised As The Opposite Gender: A non-standard case. Cal's parents did specifically want their second child to be a daughter, but bringing their baby up as a girl was clearly because of mistaking it as one, with no intention of forcing fake gender identity.
Romantic Two-Girl Friendship: At Calliope's all girls school this is stated to be common.
The Runaway: Calliope becomes one after realizing that they intend to surgically alter her body, so he cuts his hair, remakes himself as Cal and ends up in San Francisco as part of a strip joint show as "Hermaphroditus" and meets another intersex woman.
Secret Keeper: Lina is this for Desdemona and Lefty, due to having secrets of her own.
Shown Their Work: The amount of research the author did on Cal's condition really shows.
The Speechless: Lefty, after his first stroke.
Tangled Family Tree: Cal's family tree looks like this due to all the incest tropes above.
Transsexual: Cal goes through a similar process when he decides to start living as male.
What Happened to the Mouse?: In story, Cal comments that people are probably wondering what happened to Desdemona since she seemingly drops out of the story. Turns out that she's still alive and has just retreated to her room, and lives long enough to see Cal's new male persona and confess the reason he's the way he is.
Wrong Genetic Sex: As the result of 5-alpha-reductase deficiency. Genetically, Callie is 46,XY, but lacks the enzyme that converts testosterone to its active form. Thus, he has cryptorchid (undescended) testes, no ovarian or uterine structures, a nonfunctional vaginal pouch, and a microphallus (such that it's repeatedly mistaken for a larger-than-normal clitoris, both by Callie and by several doctors).
- Also applies to Zora, affected by complete androgen insensitivity syndrome, who although being able to pass as a female considers herself a hermaphrodite due to her XY chromosomes.