Determining the chimerism in stem cell transplantation (SCT) is important in the monitoring of engraftment. Conventional monitoring methods such as short tandem repeat polymerase chain reaction (STR-PCR) are labor intensive and difficult in showing the dynamics of cell subpopulations. In HLAhaploidentical SCT, flow cytometric analysis using anti-HLA antibody for the mismatched HLA can be useful in observing changes of cell subpopulations and determining chimerism. We designed a specific panel of HLA antibody reagents for the Korean population, and verified its clinical application in flow cytometric monitoring of chimerism after haploidentical stem cell transplantation. A total of 12 anti-HLA-A, -B-antibodies were selected, which could cover 82.5% of HLA-A and 16.5% of HLA-B in Korean population. This HLA panel distinguished donor and recipient cells in 22 of 23 HLA-haploidentical SCT cases. In one case, the patient had HLA-A*02/A*24, B*48/B*61 while the donor had HLA-A*02/A*33, B*44/B*48. The donor type HLA-B*44(+) and CD3(+) T cells, and HLA-B*44(+) and CD56(+) NK cells were seen at day 14 and day 8, respectively. Increased HLA-B*44(+) cells throughout the study period indicated the engraftment of donor stem cells. We were able to design a population specific panel of HLA-antibodies, and verified that flow cytometric analysis using HLA antibody for the detection of chimerism in HLA-haploidentical SCT was a simple and sensitive monitoring technique. This method allowed us to observe the dynamic changes in cell subpopulations after HLA-haploidentical SCT. Flow cytometric analysis can be considered as a strong tool for the monitoring of engraftment in HLA-haploidentical SCT.