Thirty-eight sex-mismatched bone marrow transplantation patients with various hematological diseases were followed-up using fluorescence in situ hybridization. Probes specific for various translocations, the X chromosome (DXZ1) and the whole Y chromosome (WCP Y), were used to assess successful engraftment and residual host cells. The combination of translocation and WCP Y probes enabled the identification of host and donor cells in addition to the identification of malignant vs. normal cells in the transplant recipient. Fifteen patients were sequentially followed up. The results obtained using the combination of translocation plus WCP Y probes were more reliable than those with DXZ1 plus WCP Y probes, or the translocation probe alone, especially when the percentage of residual leukemic cells detected by the translocation probe alone was around the cut-off level.