We trace the lives of several of Jonathan's ancestors, primarily Brod and Safran. Recording memories and dreams is an integral part of Trachimbrod's culture. The shtetl itself is divided into the Jewish Quarter and the Human Three-Quarters. They are divided into the Uprighters, who are more traditional, and the Slouchers, who are more secular. The people of Trachimbrod live simple lives, unconcerned with the government. Every year, they celebrate Trachimday and recreate the accident as part of the festivities. From then on, the lore of Trachimbrod revolves around the incident.

Trachim B dies, though a newborn baby survives. In 1791, a wagon supposedly belonging to a man named Trachim B crashes into a river. Letters from Alex to Jonathan reveal the two characters' growing relationship as writers and friends. Chapters written by Alex describe Jonathan's present trip. Chapters written by Jonathan describe different events in his family's history in Trachimbrod. The novel is comprised by three basic narratives: chapters written by Jonathan, chapters written by Alex, and letters from Alex to Jonathan. Accompanying the men is Grandfather's seeing-eye dog, Sammy Davis, Junior, Junior. Their driver is Alex's grandfather, who claims to be blind.

Jonathan's guide on his trip is Alex, a young Ukrainian man. He has only a few maps and a photograph of a woman named Augustine, who is said to have saved his grandfather from the Nazis. Jonathan, who has the same name as the book's author, is attempting to find his grandfather's shtetl, Trachimbrod. Everything is Illuminated chronicles a young, Jewish-American writer's attempt to research his grandfather's life in Ukraine.

Safran foer everything is illuminated