Stable cell surface presentation of MHC class I molecules requires active transport of antigenic peptides across the endoplasmic reticulum by products of two genes, TAP1 and TAP2, which are maped in the MHC class II region. There are many human diseases whose onset are associated with particular MHC alleles. However it has not always been possible to assign susceptibility to individual genes because genes within the complex are in linkage disequilibrium. In this study, we tested DNA from sixty-three healthy controls and 64 Insulin Dependent Diabetes Mellitus: IDDM patients by Polymerase Chain Reaction-Sequence Specific Oligonucleotide: PCR-SSO, Polymerase Chain Reaction-Single Strand Conformation Polymorphism: PCR-SSCP analysis and DNA sequencing. These studies demonstrated the difference in frequencies of TAP2 gene products between healthy control and IDDM patient, and between Japanese and Caucasian population. Statistic analysis of HLA antigens and variants amino acids of TAP showed the linkage disequilibrium between TAP2-665, -687 sequence and HLA-DR alleles. The data suggests that the association of TAP2 allele with IDDM disease may be a simple reflection of the linkage disequilibrium between TAP allele and DR4 gene.