AbstractObjectiveTo define the contribution of HLA genes other than HLA–B27 in conferring susceptibility to ankylosing spondylitis (AS), through analysis of HLA–B27 haplotypes in Sardinian subjects.MethodsNinety‐eight patients with AS, 133 HLA–B27–positive controls (of whom 33 were positive for HLA–B*2709), and 190 randomly selected controls were genotyped for microsatellites and single‐nucleotide polymorphisms (SNPs) spanning the HLA region.ResultsHaplotypes carrying either the B*2705 or the B*2709 allele were found to share a conserved region downstream of the HLA–B gene and a functional polymorphism in the HLA–E gene (R128G), while differing in all other markers. Notably, the presence of an A at SNP rs1264457, encoding for Arg‐128, was significantly increased in the cohort of patients (P= 6 × 10−6, correctedP= 3 × 10−5) but not in B*2705‐ or B*2709‐positive controls. Comparing the alleles co‐occurring at each HLA marker, we identified a region differentiating patients with AS and B*2705‐matched controls. In particular, there was a markedly increased prevalence of heterozygosity at rs1264457 among B27‐positive controls (74%, versus 47% in patients and 54% in random controls), suggesting a protective role of G128 in AS. Moreover, other markers around the HLA–B gene were also differentially represented.ConclusionThese results demonstrate a significant difference in the frequency of some HLA markers between AS patients and B*2705‐positive controls, which could be attributed to the opposite chromosome. In particular, the differential distribution of a functional polymorphism in the HLA–E gene suggests a possible role of natural killer function in AS pathogenesis.