A 21-year-old man with mitochondrial encephalomyopathy underwent surgery for removal of a maxillary cyst. During the induction of anesthesia, the patient fell into the state of apnea after intravenous administration of fentanyl 100 microgram. Trachea was successfully intubated followed by propofol 50 mg without any muscle relaxants. Anesthesia was maintained uneventfully under sevoflurane (1-2%), nitrous oxide (30%), and oxygen (70%). The respiratory depression lasted for about 120 minutes after administration of fentanyl, and was antagonized by naloxone 40 microgram. This case suggests that careful administration of fentanyl is mandatory in a patient with mitochondrial encephalomyopathy.