We report a patient with CML in relapse after a sex-mismatch bone marrow transplant who was treated with donor lymphocyte infusions and developed severe marrow aplasia 3 months later. As cytogenetic analysis at this point was not possible because of the very low number of marrow cells available, we used in situ hybridization (ISH) for sex chromosomes and the BCR/ABL gene together with quantitative PCR to monitor the patient's response. The results suggest that recovering haemopoiesis was derived from donor cells and contributed to the decision not to transfuse donor marrow cells on a second occasion.