Previous studies have shown that insulin-dependent diabetes mellitus is positively associated with HLA-DR4 and HLA-DR9 in Japanese populations. It was proposed that susceptibility to the disease is determined by a single HLA allele associated with both DR4 and DR9. DR genotypes in a Japanese population with insulin-dependent diabetes mellitus were determined by DRB/DQB RFLP analysis. A single disease-susceptibility-allele model was tested by the antigen-genotype-frequency-among-patients method. Recessive and additive inheritance of a single susceptibility allele were rejected. The DR9-associated disease-susceptibility allele in Japanese subjects is distinct from both the DR3- and DR4-associated susceptibility alleles in white Caucasians. The data suggest further complexity in the inheritance of HLA-associated susceptibility to insulin-dependent diabetes mellitus.