BACKGROUND We aimed to assess the potential association of runt-related transcription factor 3 (RUNX3) gene variants with ankylosing spondylitis (AS) susceptibility among Chinese Han people. MATERIAL AND METHODS Genotyping for RUNX3 variants was accomplished through polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in 115 AS patients and 102 healthy controls. Genotypes distributions of the polymorphisms in controls was assessed for their deviation from Hardy-Weinberg equilibrium (HWE). Moreover, odds ratio (OR) with 95% confidence interval (95%CI) was achieved using chi-square analysis to evaluate AS risk related to RUNX3 polymorphisms. Additionally, logistic regression analysis produced adjusted OR values. RESULTS Genotypes distribution of rs760805 and rs11249206 polymorphisms conformed to HWE in the control group (P>0.05). TT genotype of rs760805 appeared more frequently among AS cases than in controls (P=0.033), indicating its significant association with increased risk of AS onset (OR=2.309, 95%CI=1.069-4.892). The carriage of T allele in rs760805 also heightened AS incidence, in comparison to A allele (OR=1.578, 95%CI=1.075-2.316, P=0.020). Moreover, the carriage of AT+TT genotype in rs760805 and TT genotype in rs11249206 obviously increased risk of AS onset (OR=2.585, 95%CI=1.062-6.288). CONCLUSIONS RUNX3 rs760805 polymorphism can contribute to AS incidence in Chinese Han people. The interaction of the 2 polymorphisms may be a risk factor for AS.