"The film begins with the antagonist, Dr. Heiter, kidnapping a truck driver by the side of a road. Later, two US tourists, Lindsay and Jenny, arrive at Heiter's house as they search for help after getting a flat tire. Heiter quickly drugs the women, when they awake they find themselves beside the kidnapped trucker in a makeshift hospital ward in the doctor's basement. Heiter informs the trucker that he is not a match for the women and kills him. When the women next wake, the trucker has been replaced by a new captive, Japanese tourist Katsuro.
The doctor explains to his captives that he is a world-renowned expert at separating conjoined twins, but dreams of making new creatures that share a single digestive system by joining separate individuals via their mouths and anuses. He explains that his previous experiment, a creature made of three dogs, died. However, he explains how he will attach the three human subjects to each other to form what he refers to as a human centipede. The doctor then explains in great detail to his captives exactly how he will go about surgically connecting them. Once the surgery is complete, the doctor begins training his centipede to perform tasks. Katsuro, as the front part of the centipede, refuses to do as he is told, and the doctor beats him. When Katsuro defecates, Lindsay is forced to swallow his excrement and the doctor watches with great delight. However, Heiter eventually becomes irritated after being kept awake by the constant screaming of his victims and realizing that Jenny is dying from blood poisoning.
Two police detectives, Kranz and Voller, visit Heiter to investigate the disappearance of tourists in the area. After the detectives leave, Heiter informs his captives that Jenny will soon be replaced by two new parts. Katsuro stabs him with a scalpel and fails an attempt to rip out Heiter's jugular vein with his teeth, and the centipede attempts to escape as Heiter crawls after the trio. Katsuro faces the doctor with a piece of broken glass in his hand and says that he deserved to become an insect because he treated his family poorly. He then kills himself with the glass. At this point, the police officers break into the house, and Heiter crawls away to hide in the room with his swimming pool. Kranz is shocked as he discovers Heiter's victims and soon finds Voller dead in the swimming pool near an armed Dr. Heiter. Heiter and Kranz shoot and kill each other. Jenny finally dies from her blood poisoning, leaving Lindsay alone in the house, trapped between her deceased fellow captives."