Disparity of minor histocompatibility antigens (mHAs) is known to induce graft-versus-tumor and graft-versus-host disease reactions in stem cell transplantation. Not much information is available on genotypic and phenotypic distributions of the currently identified mHAs, especially in Korean population. Therefore, we report genotype and phenotype frequency analyses of 10 autosomal mHAs in 329 unrelated healthy Koreans using the Sequenom MassARRAY matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) system and polymerase chain reaction-sequence specific primers (PCR-SSP). Estimates of the probability of immunogenic mismatches between donor/recipient pairs were made from observed phenotypic frequencies. HA-1 was the most favorable mHA for clinical application with the highest disparity of 7.0%. Similar results were obtained in ACC-1. The Korean population can benefit the most in a setting of matched major histocompatibility complex (MHC)-restricted mHAs-mismatched unrelated hematopoietic stem cell transplantations with the disparity rate of 27.5% with eight hematopoietic mHAs. This is the first comprehensive report on the genotypic and phenotypic frequency distributions of human mHAs in the Korean population. It can contribute to not only donor selection before transplantation but also therapeutic approaches after transplantation. It is expected that mHA-based immunotherapy will lead to a new treatment modality tailored for patients at high risk of relapse following allogeneic hematopoietic cell transplantation.