A rare case of medulla oblongata germinoma in a 19-year-old Japanese man with Klinefelter syndrome is presented. Light microscopic examination of the resected specimen showed very few lymphocytes, and an immunohistochemical study for placental alkaline phosphatase was of great diagnostic value. Up to now there have been only five cases of intracranial germ cell tumors in association with Klinefelter syndrome. These tumors were situated along in the midline structure. It is emphasized that endocrinological factors at the time of embryogenesis as well as a genetic malignant potential are important in the pathogenesis of extragonadal germ cell tumors associated with Klinefelter syndrome.