A 12 year-old girl with juvenile myelomonocytic leukemia (JMML) and monosomy 7 underwent allogeneic bone marrow transplantation (BMT) from her HLA-matched brother. To monitor the engraftment and the course of the disease we used fluorescence in situ hybridization (FISH) with probes specific for the centromeres of chromosomes X, Y and 7. Complete hematological remission was achieved and confirmed by the virtually exclusive presence of normal male cells in the bone marrow (BM). Acute graft-versus host disease (GvHD) was treated with prednisone and cyclosporine A (CSA) and female cells with monosomy 7 reoccurred in the peripheral blood (PB) and BM. After discontinuation of the immunosuppressive therapy, the leukemic cells with monosomy 7 disappeared again from these compartments. One year after transplantation, isolated extramedullary relapses occurred in lymph nodes and skin, followed by dissemination of blast cells into the BM, whereas the PB cells remained of donor origin. The fact that the leukemic cells fluctuated with the intensity of the immunosuppressive treatment provides evidence of a graft versus leukemia (GvL) effect in this unusually old girl with JMML with a unique extramedullary disease progression.