AIM: To explore the association of single nucleotide polymorphisms (SNPs) in the IL33/IL1RL1 gene region with the susceptibility to Behcet’s disease (BD) in a Chinese Han population. METHODS: A total of eight SNPs in the candidate gene region (rs11792633, rs7025417, rs10975519 and rs1048274 in IL33; rs2310220, rs12712142, rs13424006 and rs3821204 in IL1RL1) were genotyped in783 BD patients and 701 healthy controls by the Sequenom Mass Array iPLEX platform. RESULTS: A statistically significant association was observed between IL1RL1 rs12712142 and BD patients. The frequency of IL1RL1 rs12712142 variant allele A was significantly lower in BD patients than that in controls (OR=0.8, 95%CI: 0.69-0.94, Pc=0.039); the genotype distribution (Pc=0.043) and additive and dominant genetic model analyses (OR=0.8, 95%CI: 0.69-0.94, Pc=0.040 and OR=0.72, 95%CI: 0.58-0.88, Pc=0.011) also indicated a strong association between rs12712142 and BD patients. CONCLUSION: This is the first study to reveal the association between IL1RL1 rs12712142 variant allele A and the decreased risk of BD in the Chinese Han population, indicating a protective role of IL1RL1 in the pathogenesis of BD.