Serological studies have suggested the presence of a new HLA-B39 subtype (B39.2) in the Japanese population. To identify the new HLA-B39 subtype and compare it with an other HLA-B39 subtype (B39.1), the genes encoding HLA-B39.1 (B*39013) and B39.2 (B*3902) have been cloned from Japanese. We have sequenced these genes and completed the sequence of HLA-B39.1 (B*39011) gene from a Caucasian that was partially sequenced. Comparison of the sequence data revealed that B*3902 and B*39013 differ by three nucleotide substitutions which result in a two amino acids change at residues 63 and 67, while one silent substitution at codon 312 is found between B*39011 and B*39013. These results suggest that B*3902 has evolved from B*39013 rather than B*39011.