Non-syndromic oral cleft is one of the most common congenital malformations, and more than 40 genes may be involved in its aetiology. Recent studies have shown that the Wnt10a gene may also contribute. We recruited 198 patients with non-syndromic oral clefts, comprising 96 elementary families (restricted to the patients and their parents) and 187 controls, to investigate their associations with the risk of such clefts and their subgroups in a Chinese Han population. The variant evaluated in this study was a single nucleotide polymorphism - specifically, a missense mutation C392T of Wnt10a. Polymerase chain reaction (PCR) restriction fragment length polymorphism (RFLP) was used to genotype the marker, and case-control and family-based associations were analysed. Although in the case-control study there were no significant differences in frequency distributions of genotypes or alleles between cases and controls in the groups with cleft palate and cleft lip and palate, the genotypic and allelic frequencies of C392T in the total groups and the group with cleft lip alone differed significantly from those in the controls (p=0.04, and 0.01, respectively). A transmission disequilibrium test showed a transmitted disequilibrium in C392T. In conclusion, we found an association between the C392T variant and non-syndromic oral clefts.