We here identified a novel HLA-A allele, A*030104, which was found in a Japanese family. The direct sequencing revealed that A*030104 was identical to A*030101 except for a nucleotide substitution of GAG to GAA at codon 63 without an amino acid replacement. The frequencies of A*030104 and A*0301 including A*030104 in Japanese population (n = 22,360) were approximately 0.013 and 0.40%, respectively.