Allogeneic hematopoietic stem cell transplantation (HSCT) is an effective therapeutic approach for several hematological diseases. Chimerism studies can be helpful to assess donor engraftment, detect early signs of graft rejection, and monitor minimal residual disease. Currently the most common method for monitoring chimerism following HSCT is by PCR amplification of STR loci followed by capillary electrophoresis. Prior to transplantation, multiple STR loci in both the donor and recipient are analyzed in order to identify loci that differentiate the two individuals. Informative loci are selected to calculate the percent donor and recipient present in post-transplant specimens. This is a rapid, sensitive, and cost-effective method for monitoring chimerism in patients following HSCT.