A human leukocyte antigen (HLA)-matched unrelated donor is the primary alternative donor for allogeneic hematopoietic cell transplantation in Japan. In considering an optimal donor registry size, the availability of HLA-matched donors is important. In this study, the probability of finding an HLA-A, -B, -C, and -DRB1 allele-matched donor was estimated using two different methods based on the haplotype frequencies in the Japanese population: an actual measurement method (AMM) and a formula method (FM). According to AMM, the probabilities of finding an HLA-matched donor were 40.5% in 100,000 donors, 54.4% in 300,000, 60.0% in 500,000, and 63.4% in 700,000. On the other hand, according to FM, the probabilities were 47.8% in 100,000 donors, 59.9% in 300,000, 65.3% in 500,000, and 68.8% in 700,000. The probabilities increased by 8.6 or 7.7%, 3.2 or 3.1%, 2.1 or 1.9%, and 1.6 or 1.3% in AMM or FM, respectively, as the registry size increased by 100,000. The rate of increase in the probability of finding an HLA-matched donor will become smaller as the registry size increases due to the diversity of haplotypes. Therefore, it is important to set a target donor registry size for efficient donor recruitment by considering the haplotype frequencies in the population.