Abstract Introduction The aim of this study was to characterize the association of human leukocyte antigen (HLA) B alleles and major histocompatibility complex (MHC) single nucleotide polymorphisms (SNPs) with Behçet’s disease (BD) in an Iranian dataset. Methods The association of three SNPs in the MHC region previously identified as the most associated in high-density genotyping studies was tested in a case–control study on 973 BD patients and 825 controls from Iran, and the association of HLA-B alleles was tested in a subset of 681 patients and 414 controls. Results We found that HLA-B*51 ( P  = 4.11 × 10 −41 , OR [95% CI] = 4.63[3.66-5.85]) and B*15 confer risk for BD ( P  = 2.83 × 10 −2 , OR [95% CI] = 1.75[1.08-2.84]) in Iranian, and in B*51 negative individuals, only the B*15 allele is significantly associated with BD ( P  = 2.51 × 10 −3 , OR [95% CI] = 2.40[1.37-4.20]). rs76546355, formerly known as rs116799036, located between HLA-B and MICA (MHC class I polypeptide-related sequence A), demonstrated the same level of association with BD as HLA-B*51 ( P adj  = 1.78 × 10 −46 , OR [95% CI] = 5.46[4.21-7.09], and P adj  = 8.34 × 10 −48 , OR [95% CI] = 5.44[4.20-7.05], respectively) in the HLA-B allelotyped subset, while rs2848713 was less associated ( P adj  = 7.14 × 10 −35 , OR [95% CI] = 3.73[2.97-4.69]) and rs9260997 was not associated ( P adj  = 1.00 × 10 −1 ). Additionally, we found that B*51 genotype-phenotype correlations do not survive Bonferroni correction, while carriers of the rs76546355 risk allele predominate in BD cases with genital ulcers, positive pathergy test and positive BD family history (2.31 × 10 −4  ≤  P  ≤ 1.59 × 10 −3 ). Conclusions We found that the HLA-B*51 allele and the rs76546355/rs116799036 MHC SNP are independent genetic risk factors for BD in .