We report a case of a 67-year-old man with clear cell adenocarcinoma of the remnant uterus in persistent Müllerian duct syndrome. He had a normal penis, urethra, and scrotum, and there was also a vagina and uterus. He died in a traffic accident, and clear cell adenocarcinoma was discovered incidentally at autopsy. Clear cell adenocarcinoma of the remnant uterus metastasized to the retroperitoneal lymph nodes and bilateral lungs. Persistent Müllerian duct syndrome is characterized by the persistence of Müllerian derivatives in otherwise normally virilized males. A variety of germ cell tumors of the testis have been reported in association with persistent Müllerian duct syndrome. However, no malignant change of the persistent Müllerian duct structures has been reported. This represents the first reported case of malignant change of the persistent Müllerian duct structures in persistent Müllerian duct syndrome.