Clinical trial of organ transplantation was renal transplantation by Voronoy at 1936. The discovery of HLA in the 1950s was one of the most important new findings in the area of transplantation. Nowadays, developing HLA genotyping methods, the serum analysis does not use for donor and recipient HLA typing but for cross-matching test. Because each of HLA genotyping methods has its merits and demerits, it is important to choice right methods for avoiding type error. PCR-Luminex method using fluorescence microsphere was developed for high-resolution HLA-A, HLA-B and HLA-DRB1 genotyping in the Japanese population. This genotyping method allows to define all the possible combinations of alleles at each loci existing in Japanese at the four-digital level. In hematopoietic stem cell transplantation, to match high resolution level of HLA between donor and recipient lead an improvement of recipient's survival. In organ transplantation, removed organ has to be so immediately transplanted into recipient that no time is left for HLA genotyping. In order to have good survival of transplanted organ, HLA, cytokine promoter lesion and immunoglobulin like receptor genotyping might be helpful. We focused on this review at HLA genotyping, especially new SSO methods.