HLA-DM molecules are involved in the antigen-processing pathway of HLA class II-restricted antigen presentation. We investigated polymorphisms of HLA-DM genes in atopic dermatitis by using the polymerase chain reaction-restriction-fragment length polymorphism method to examine a possible contribution of these genes to the pathogenesis of atopic dermatitis. Genomic DNA was extracted from 37 Japanese patients with atopic dermatitis and 52 control subjects. After polymerase chain reaction amplification of the polymorphic third exon of DMA and DMB genes, amplified products were digested with restriction endonucleases to determine HLA-DM alleles. FokI, HinfI, AciI and SfaNI were used for DMA; HhaI, BsrI, ApaLI, and Bsp1286I for the DMB gene. We identified three DMA alleles and also three DMB alleles. One of 37 patients possessed the DMA*0103 allele, which has been reported as a rare allele in Caucasian populations. Any DMA and DMB alleles were not increased in the patients. The DMA*0102 allele was estimated to constitute a haplotype with DRB1*1201/DQB1*0301 and DRB1*0901/DQB1*0301 in a Japanese population. HLA-DM genes are not considered to contribute primarily to the susceptibility of atopic dermatitis. Further investigation of the functional roles of HLA-DM gene polymorphisms will be useful for a better understanding of susceptibility loci in HLA class II-associated disease.