Middlesex, a Pulitzer Prize winning novel by Jeffrey Eugenides, spans the lives of three generations of the Stephanides family. Protagonist Calliope (Cal) Stephanides undergoes a spiritual rebirth as he comes to terms with his family’s history and how it inevitably led to his hermaphroditic birth. The story takes place in 1922 in Bithynios, Greece. Lefty and Desdemona Stephanides, brother and sister, have lost their parents in the recent war with Turkey. They have an unhealthy attraction to one another. When the Turks move to reclaim their village, Lefty and Desdemona flee, traveling first to Smyrna and then sailing to America. Along the way, they pick up an Armenian, Dr. Philobosian, who lost his entire family in the Turkish invasion. Being anonymous on the ship, Lefty and Desdemona act out an elaborate courtship and get married.

The Stephanides lose Dr. Philobosian at Ellis Island and take a train to Detroit to live with their cousin Sourmelina (Lina), who is a closet lesbian, and her husband Jimmy Zizmo. They swear Lina to secrecy about their relationship. Jimmy, a rum-runner, gets Lefty a job at the Ford factory, but Lefty is fired because of Jimmy’s unsavory reputation. At the same time, both Desdemona and Lina become pregnant. Desperate for cash, Lefty helps Jimmy import booze. Dr. Philobosian finally arrives in Detroit. He inadvertently fills Desdemona with fear about inbred babies.

Lina gives birth to a healthy girl, Theodora (Tessie). Jimmy is paranoid that Lina has had an affair. Desdemona gives birth to Milton, an equally healthy boy, at the same time. Lefty opens a speakeasy in the basement to support the family. After the repeal of prohibition, he turns it into legitimate bar called The Zebra Room.

When Milton and Tessie reach the age of twenty, they begin a strange musical courtship. Desdemona, ever fearful of genetics, tries to keep them apart. After Tessie becomes engaged to Mike Antoniou, a soon-to-be Greek Orthodox priest, a devastated Milton joins the Navy. He is stationed in San Diego. Watching the newsreels at home, Tessie realizes her true feelings. Milton comes home safely. Much to Mike's chagrin, Tessie and Milton get married. Mike is left to marry Zoe. Milton takes over the Zebra Room, turning it into a neighborhood diner. He and Tessie have a son. Then, they decide they want a daughter, so they use “science” to manipulate biology to their will. Desdemona predicts they will have another son, but Calliope is born a healthy baby girl. Dr. Philobosian, who delivers her, fails to notice she is a hermaphrodite. On the same day Callie is born, Lefty has the first of a series of strokes, rendering him mute.

As the neighborhood becomes shabby and the family faces financial ruin, race riots destroy The Zebra Room, giving Milton the insurance capital to start a successful hot dog chain. The family moves to the well-to-do suburb of Grosse Pointe, where eight year old Callie meets a little girl named Clementine. Clementine's kisses give Callie the idea that she is different from most girls. At the same time, Lefty dies. Desdemona takes to her bed permanently.

At age fourteen, Callie is attending a private school for girls when she falls in love with a girl she calls the Obscure Object. The girls start a secret sexual relationship. Jerome, the Object’s jealous brother, guesses their secret and causes Callie to have an accident. In the emergency room, doctors finally discover her double genitalia. Shocked, Milton and Tessie take her to New York City to see a specialist, Dr. Luce. Callie, wanting to be normal, lies to Dr. Luce about her feelings, and he recommends that Callie continue to live as a girl. But, Callie sees the report describing her as genetically male. Knowing her true feelings, she runs away.

Cutting her hair and calling herself Cal, he arrives in San Francisco where he works in a strip club for a man named Bob Presto. Cal meets another hermaphrodite and starts to accept himself. When the club is raided and Cal is arrested, he finally calls his parents, only to discover Milton is dead. He was killed in an automobile chase after being the victim of a kidnapping scam.

Chapter Eleven retrieves Cal from California. He takes his new gender in stride. Arriving home, Tessie has a harder time dealing with it. However, she wants to accept Cal out of maternal love. Desdemona, in a rare moment of lucidity, reveals the genetic map that led to Cal’s condition. While the others attend Milton’s funeral, Cal acts out the traditional Greek rite of keeping Milton’s spirit from returning to the house.

Cal writes his memoir in 2001 while working for the Foreign Service in Berlin. He meets an Asian-American woman, Julie Kikuchi, whom he likes very much. Before things get serious, he cuts Julie out of his life. However, when they run into each other at an art exhibit, he gathers the courage to reveal that he is a hermaphrodite. They agree to give their relationship a real chance.