To determine the impact of imatinib therapy prior to allogeneic stem-cell transplantation in advanced stage chronic myelogenous leukaemia (CML), 30 CML patients who had received imatinib as part of pre-transplant treatment were analysed, with special emphasis on the cytogenetic response to imatinib therapy shortly before transplantation. Median patient age was 51 years (range, 24 - 64). At the time of transplantation all patients were in second or higher chronic phase (CP). The median follow-up after allogeneic transplantation was 360 days (range, 24 - 1524). Cox regression analysis revealed that the quality of cytogenetic response was a prognostic factor for transplant-related mortality (p = 0.050), relapse incidence (p = 0.015), leukaemia-free survival (p = 0.002) and overall survival (p = 0.006). A cytogenetic response with <35%BCR-ABL-positive interphase nuclei in FISH analysis from bone marrow was associated with a probability of overall survival of 81% at 3 years. In conclusion, our data suggest that advanced stage CML has an excellent outcome after allogeneic haematopoietic stem-cell transplantation when transplanted in the phase of cytogenetic response to imatinib.