Relapse of the underlying malignant disease represents one of the major causes of treatment failure in patients treated with stem cell transplantation, especially in patients with acute leukemia. Detection of minimal residual disease (MRD) after allogenic stem cell transplantation (SCT) is important to schedule therapeutic intervention, e.g. donor lymphocyte infusion. We asked, whether chimerism analysis in circulating CD34+ cells might be a feasible method to monitor MRD in patients after allogeneic SCT. Eighty-seven patients undergoing allogeneic SCT were prospectively analyzed. CD34+ cells were prepared from peripheral blood samples and sorted after immunomagnetic preenrichment. Results were correlated to overall chimerism and results of nested RT-PCR for the bcr-abl rearrangement in Ph1-cases. In the 87 patients a median of 8 analyses (range 2-22) covering a median period of 295 days (range 28-1152) were performed. A hematological relapse was observed in 22/84 engrafting patients (26%). In twenty patients, the relapse was detected in the CD34+ fraction, in 14 of these patients, donor chimerism in CD34+ cells decreased 12-97 days (median 52 days) before the clinical diagnosis. In two cases, CD34+ chimerism failed to demonstrate the relapse. In patients with relapsing CML, the decrease of donor CD34+ cells was associated with reappearance of bcr-abl transcripts. Treatment (reduction of immunosuppression, DLI or STI571) was associated with an increase of donor derived CD34+ cells and clearance of bcr-abl positive cells. Sequential chimerism analysis in CD34+ cells is feasible and sensitive, allowing early detection of relapse and monitoring of therapeutic intervention. This method appears especially useful in patients with high risk leukemia lacking other markers for detection of MRD.