Patients who develop mixed hematopoietic chimerism (MHC) after allogeneic bone marrow transplantation (allo-BMT) might have an increased risk of relapse or graft failure. In order to identify patients with MHC we established a quantitative polymerase chain reaction (PCR) approach to estimate the individual degree of autologous recovery and investigate the dynamics of MHC posttransplant. Therefore standardized mixed chimeric samples were generated in each individual case by mixing pretransplant recipient and donor DNA at a range of percentages. After amplification the samples were analyzed densitometrically and signal intensities were taken as the basis of individual standard curves. Subsequently posttransplant DNA samples were also analyzed, the intensity of the informative signals were compared to the standard curves and autologous recovery was expressed in percentage related to host DNA. We investigated 40 pediatric patients receiving allo-BMT by this method. 10/40 developed MHC during course of the observation period. Each patient with MHC revealed a certain dynamic. This approach might be helpful when deciding on early intervention and additional treatment to prevent graft failure or relapse.