We examined polymorphisms of transporter associated with antigen processing (TAP) genes in 37 Japanese patients with atopic dermatitis and 52 control subjects. We have evaluated, again, the specificity polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method since our previous report and have also developed a mismatch PCR-RFLP method for discriminating two dimorphic sites of TAP1 gene and four dimorphic sites of TAP2 gene. Amplified products from genomic DNA were digested with restriction endonucleases: Sau3A1 for TAP1 codon 333 (Ile-Val), AccI for TAP1 codon 637 (Asp-Gly), and BfaI for TAP2 codon 687 (Stop-Gln). The other sites of TAP2 gene were analyzed by mismatch PCR-RFLP: AccII for TAP2 codon 379 (Val-Ile), RsaI for codon 565 (Ala-Thr), and MspI for codon 665 (Thr-Ala). We observed three TAP1 alleles and six TAP2 alleles. Infrequent allele TAP1 C was observed in one patient and one control subject. We did not identify any differences in TAP allele frequencies between those patients with atopic dermatitis and Japanese control subjects. Analysis of TAP gene polymorphisms will provide better understanding of susceptibility loci in HLA class II-associated disease because TAP genes are located between HLA-DQB1 and HLA-DPB1 loci.