Insulin dependent diabetes mellitus (IDDM) is a classical organ-specific autoimmune disease of the pancreatic beta cells. We have previously reported that HLA-B61, along with HLA-B54 and DRB I *0405, was associated with IDDM in a Japanese population, suggesting the presence of an HLA-B-1inked risk factor which is independent of HLA-DRIDQ alleles. Because HLA-B6 1 antigen is encoded by two major B40-related alleles, B*4002 and B*4006, in Japanese, we re-examined the association with the HLA-B polymorphisms, and analyzed the microsatellite loci flanking to the HLA-B Iocus. The results indicated that the frequencies of both B*4002 (21. 6% vs. 12. 2%, OR=1. 99, P=0. 023, 95% CI=1. 09-3. 63) and B*4006 (19. 4% vs. 10. 5%, OR=2. 06, P=0. 024, 95% CI= 1. 09-3. 88) were increased in the patients, and that two microsatellite markers, C 1_4_1 and C 1_2_5, showed strong associations with IDDM. In addition, haplotypic association studies suggested that the HLA-B itself, not the flanking regions linked to the microsatellite alleles, conferred the risk of IDDM.