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We present the case of a young male with a mediastinal non-seminomatous germ cell tumor who developed a severe thrombocytopenia, one year after initial diagnosis and surgical treatment and chemotherapy. Bone marrow morphology suggested myelodysplastic syndrome (refractory cytopenia with multilineage dysplasia). Cytogenetics of bone marrow showed near tetraploid karyotype, raising concerns about the diagnosis of MDS. The patient died within one month due to refractory disease and autopsy revealed a highly invasive germ cell tumor in the mediastinum and chest wall which showed the same cytogenetic abnormality seen in the bone marrow. The bone marrow collected at autopsy showed features compatible with acute myeloid leukemia. The implications of this transdifferentiation of a mediastinal germ cell tumor into an apparent hematological malignancy for correct diagnosis and appropriate treatment are discussed.