<p>Background: Nonsyndromic cleft lip and/or palate (NSCL/P) is the most common orofacial birth defect, often attributed to ethnic and environmental differences. Up to now, linkage analyses and genome-wide association studies have identified several genomic susceptibility regions for NSCL/P. The <em>WNT</em> genes including <em>WNT3</em> are strong candidates for NSCL/P, since they are involved in regulating mid-face development and upper lip fusion. This study tested association of the WNT3 polymorphisms, rs3809857 G/T and rs9890413 G/A, with the risk of NSCL/P in a population of Iranian infants.<br /> Methods: The allelic and genotypic frequencies for each participant were determined in 113 unrelated Iranian subjects with NSCL/P and 220 control subjects using PCR and restriction fragment length polymorphism (RFLP) methods. A p-value of 0.05 was considered statistically significant.&nbsp;<br /> Results: The <em>WNT3</em> rs3809857 GT genotype was significantly lower (p=0.039, OR=0.55, 95% CI=0.30-0.97) in the NSCL/P (21.2%) than the control group (30.42%). For the WNT3 rs9890413 G/A polymorphism, neither genotype nor allele frequencies were significantly different between the case and control groups.<br /> Conclusion: Our results indicated that the <em>WNT3</em> rs3809857 GT genotype may have a protective effect against NSCL/P in Iranian population.</p>