BACKGROUND: The human platelet antigen (HPA) 1 through 5 and the human neutrophil antigen (HNA-1) systems are relevant to immune-related thrombocytopenia and neutropenia. The alloantigen distribution profiles in the population will aid in estimating the risk of alloimmunization. STUDY DESIGN AND METHODS: Genotyping of the genes that control the expression of the HPA-1 through -5 and HNA-1 systems in Taiwanese (n = 326) and Taiwan's indigenous peoples (n = 608) was performed by PCR with the sequence-specific primer (PCR-SSP) method. RESULTS: In the HPA system, HPA-1b and HPA-4b were absent among Taiwan's indigenous tribes and detected among other Taiwanese only with frequencies of <0.2 percent and <0.5 percent, respectively. The GP1BA*2 (HPA-2b) and GP1A*2 (HPA-5b) allele frequencies range from 1 percent to 7 percent and 0.4 percent to 3.5 percent among the two ethnic groups, respectively. GP2B*1 (HPA-3a) and GP2B*2 (HPA-3b) showed similar allele frequencies. In the HNA-1 system, the FCGR3B*1 (HNA-1 a) allele frequency was about twice that of FCGR3B*2 (HNA-1b) in Taiwanese and also in most of the indigenous tribes. Three FCGR3B (HNA-1) null persons were found in one indigenous tribe (Ami tribe), for an FCGR3B null frequency of 19.8 percent. However, no FCGR3B*3 (HNA-1c) allele was detected in Taiwan. CONCLUSION: The frequencies of HPA-1b, -2b, and -5b in the Taiwanese population were much lower than those among whites. In Taiwan, all of the HNA-1 null found was due to the deletion of the FCGR3B gene, and this deletion may be widely distributed in the Ami tribe.