Several methods have been used to evaluate engraftment after allogeneic bone marrow transplantation (BMT). We assessed the usefulness of a multiple short tandem repeat (STR) amplification kit combined with a capillary electrophoresis unit for DNA identity analysis in the evaluation of engraftment after BMT. For 17 of 18 patients, at least 1 locus showed unique alleles for the donor and the recipient. In all cases, at least 1 locus was informative for the presence of small amounts of recipient DNA. The results from STR analysis were the same as Southern blot analysis in 14 of 17 cases. Differences included mixed chimerism detected only with STR analysis, informative loci present only with STR analysis, and informative loci present only with Southern blot analysis (1 case each). By using mock mixed chimeras, minor populations of 5% were detected routinely in all loci using the kit manufacturer's default protocol. By increasing the amount of amplified DNA, minor populations of 1% were detected in all cases but not in all loci. This single reaction technique provides for faster results, reduced workforce needs, and greater sensitivity than traditional Southern blot.