Abstract: Graft-versus-host disease (GvHD) can be a major complication of allogeneic bone marrow transplantation even in recipients of HLA genotype-identical transplants. Disparities in minor histocompatibility antigens (mHags) between donor and recipient are a potential risk for the development of GvHD. A mismatch for the mHag HA-1 can cause GvHD in adult recipients of allogeneic bone marrow from HLA-identical donors. The mHag HA-1, first identified by HLA -A *0201 -restricted cytotoxic T cells (CTLs), was recently chemically characterized as a nonapeptide. On the cDNA level, the HA-1 locus has two alleles, HA-1H and HA-1R, which differ in two nucleotides, resulting in a single amino acid substitution. Here we report on the genomic structure of the HA-1 locus. Isolation and sequencing of cosmid DNA encoding the HA-1 peptide sequence revealed that the HA-1 alleles are encoded by two exons. Two different primer sets were designed, each consisting of allele-specific primers and a common primer, and both sets containing intronic sequences. We performed genomic DNA typing of three families consisting of 24 HLA-A*0201 -positive individuals. The predicted allele-specific products correlated in all cases with the mHag classification by CTLs and by RT-PCR. We demonstrate for the first time the genomic identification of the mHag HA-1 locus. Prospective genomic typing for the HA-1 alleles will improve donor selection and identify HLA-A*0201 -positive recipients with a high risk for HA-1-induced GvHD.