The contribution of polymorphism of DMA and DMB alleles to the pathogenesis of Japanese Systemic Sclerosis (SSc) was studied in 55 Japanese SSc patients and 77 normal Japanese subjects using the PCR-RFLP (restriction fragment length polymorphism) method. The allele frequencies of DMB*0101 allele were increased in SSc with diffuse scleroderma (70.0% vs 49.4%, p < 0.05, pc = not significant (NS)) and in SSc with antitopoisomerase I antibody (a-Scl-70), (68.2%, p < 0.05, pc = NS). The phenotype frequencies of DMB*0101 in these subgroups of SSc were increased significantly (95.0%, p = 0.014, pc < 0.05; 95.5%, p = 0.0088, pc < 0.05, respectively). In contrast, DMB*0102 and DMB*0103 alleles tended to decrease in diffuse scleroderma and SSc with a-Scl-70, but the decreases were not significant. Association analysis among DMA, DMB, and DRB1*1502 in Japanese SSc with diffuse scleroderma and SSc with a-Scl-70 indicated that the increase in DMA*0101 was not primary, but reflected an increase in HLA DRB1*1502.