We report a patient who developed acute myeloid leukaemia (M2) shortly after successful treatment of a mediastinal germ cell tumour. The leukaemia was preceded by a documented myelodysplastic phase. Complex cytogenetic abnormalities were found in bone marrow and peripheral blood cells including +i(12p), typical of germ cell malignancy. Fluorescence in situ hybridization revealed the presence of +i(12p) in myeloblasts, erythroblasts and neutrophils but not in lymphocytes. This case provides further evidence for a common clonal origin of haematological malignancies and mediastinal germ cell tumours.