In Finland the frequency of isolated cleft palate (CP) is higher than that of isolated cleft lip (CL) or cleft lip with cleft palate (CLP). This trend contrasts to that in other countries but its genetic underpinnings are unknown. We performed a genome-wide association study for orofacial cleft, which includes CL, CLP, and CP in the Finnish population. We identified rs570516915, a single nucleotide polymorphism that is virtually specific to Finns and Estonians, as being strongly associated with orofacial cleft, and predominantly with CP (p = 5.25 x 10-34, OR = 8.65, 95% CI 6.11-12.25). The risk allele frequency for rs570516915 parallels the regional variation of CP prevalence in Finland, and the association was replicated in an independent sample of CP cases from Estonia (p < 1.3 x 10-11). The rs570516915 variant lies in an IRF6 (Interferon Regulatory Factor 6) enhancer active in ectodermal and oral epithelial cells. Other variants in the IRF6 locus, including those in the same enhancer, are associated with orofacial cleft, but predominantly with CL or CLP, suggesting shared mechanisms in the distinct processes of lip and palate development. By luciferase and transgenic mouse reporter assays we found that the risk allele of rs570516915 diminishes the activity of the enhancer. CRISPR-Cas9 edited oral epithelial cells demonstrate that rs570516915 disrupts an IRF6 binding site and decreases the expression of IRF6, suggesting impaired IRF6 autoregulation as the molecular mechanism underlying risk for CP.