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Background The axis inhibition protein 2 ( AXIN2) is an important regulator of β-catenin degradation in the Wnt pathway, which plays a key role in craniofacial morphogenesis. The goal of this study was to investigate the potential relationship between AXIN2 polymorphisms and the risks of non-syndromic orofacial clefts ( NSOC) in a Chinese Han population. Methods Four polymorphisms of AXIN2 (rs2240307, rs11867417, rs2240308, and rs7591) were selected to perform a case-control study with 599 NSOC cases and 602 healthy individuals from a Chinese Han population. The single nucleotide polymorphisms ( SNPs) were genotyped on basis of double ligation and multiplex fluorescence PCR. Results Weak associations were found between these four SNPs and the risk of NSOC. Further stratified analysis showed that the overall genotype frequencies of rs2240307 were different between the cleft palate only ( CPO) group and the control group ( P = 0.048), and GG genotype markedly contributed to the susceptibility to CPO ( OR = 3.22, 95% CI = 1.13-9.18). The similar effect was also observed on GA/ AA genotype compared with GG homozygote ( OR = 0.30, 95% CI = 0.11-0.84). The results of LD analysis between each pair of SNPs revealed that two SNPs (rs11867417 and rs7591) were in a LD block ( r2 > 0.8). But no statistically significant was found between cases and controls from haplotype analysis in these two loci. Conclusions The borderline results gave us a hint that rs2240307 contributed to the susceptibility to CPO in a Chinese Han population, which was conductive to improving our awareness of the causes of NSOC. [ABSTRACT FROM AUTHOR]