The role of genetic background in the development of Behçet's disease (BD) is best reflected by the strong association between HLA-B*51 and BD that has been demonstrated across various ethnic groups. The contributions made by other HLA or non-HLA genes to disease susceptibility have been suggested by the results of a number of gene association studies, although the true associations between the genes located within the major histocompatibility complex (MHC) region and BD have often been doubted due to the possibility of linkage disequilibrium of those genes with HLA-B*51. The presence of a true susceptibility gene in the vicinity of HLA-B*51 has also been extensively investigated because of the limited evidence that directly relates HLA-B*51 to the pathogenesis of BD. However, recent genome-wide association studies have confirmed that HLA-B*51 is primarily associated with BD and that there are multiple susceptibility loci other than HLA-B*51. In this review, we discuss BD-associated genes within the MHC region and their biological roles in the pathogenesis of BD.