We report a 39 year-old man with disseminated extragonadal germ cell tumor (GCT), whose serum level of human chorionic gonadotropin (HCG) increased again after platinum-based combination chemotherapy, high-dose chemotherapy with autologous bone marrow rescue and radical adjunctive surgery. The increase in the HCG level was progressive in spite of multiple chemotherapy, and after a while, a coin lesion in the right lung was identified by chest roentgenography. The pulmonary lesion was refractory to additional chemotherapy. After a systemic survey to confirm that the lesion was solitary, video-assisted thoracoscopic wedge resection of the right lower lobe was performed. Because the resected tumor included viable tumor cells and the serum HCG level remained slightly high one month after the operation, oral low-dose etoposide was begun. In a short time, the level of the serum tumor marker decreased and remained normal during the subsequent 7 months of therapy and thereafter. The patient remains in complete remission 13 months after completion of the final therapy and 3 years after the initial diagnosis. Even if the level of a serum tumor marker is high, salvage resection can be a promising therapeutic option for operable tumors that are refractory to chemotherapy. The usefulness of chronic oral etoposide for patients with GCT should be examined by further clinical trials.