Here, we report on a 20-year-old patient with a primary nonseminomatous mediastinal germ cell tumor (MGCT) who developed myelodysplastic syndrome (MDS) 2 months following chemotherapy with cisplatin, etoposide, ifosfamide, and paclitaxel. Bone marrow examinations revealed that the MDS was a refractory anemia with excess type II blasts and complex chromosomal abnormalities. With the onset of MDS occurring rapidly following chemotherapy, it is unlikely to have been caused by the therapy. We discuss the association between primary nonseminomatous MGCTs and hematological malignancies, including the possibility of a common clonal origin. (Korean J Med 2016;90:460-463)