The collection of stories in Let the Dead Bury Their Dead takes place in the small town of Tims Creek in North Carolina. Themes are woven across narratives in the stories, told from different generational perspectives and through different sources (conversation, diaries, extracts from sermons, and historical sources).

Homosexuality and Religion

Two interconnected themes are homosexuality and Fundamentalist Christianity, which are in direct conflict with one another. In "The Foundations of the Earth," Maggie comes to accept her dead grandson Edward's homosexuality, understanding that her church had "poisoned" her mind against her own grandson. In "Run, Mourner, Run," a white gay man named Dean Williams is paid to seduce and blackmail the wealthiest black man in town, Ray Brown, who is also homosexual.

Magical Realism

The theme of magical realism is present in multiple stories, most notably the first and last, which emphasizes the prominence of supernatural spirits in the book overall. In "Clarence and the Dead," Clarence Pickett converses with townsfolk who have been dead for generations before his death. "Let the Dead Bury Their Dead" tells the story of the founding of Tims Creek by escaped slaves, who rise up after the Civil War to attack the living townspeople.

Racism

Multiple stories contain the theme of racial discord between white people and black people in the context of the post–Civil Rights era. The town of Tims Creek has a predominantly black population, and throughout the stories there is a racial distrust from both perspectives. Sexual passion is also explored in socially unacceptable circumstances, including extramarital affairs and incest. In "Ragnarok! The Day the Gods Die," Reverend Barden presents a respectful eulogy on a woman that had once been his lover. The pious words he says to the congregation are broken up with internal reflections in brackets, in which he expresses his deep shame and spiritual uncleanliness. Similarly, in "Cornsilk," Aaron indulges in fantasies about the sexual affair he had with his half-sister, Jamonica. In Randall Kenan's stories, there is a strong sense of multiple interpretations of reality; there is the spiritual world, full of God, angels, demons, and ghosts; the physical world in which individuals present themselves; and the internal world of forbidden thoughts, regret, and shame.