Orofacial clefts are congenital structural anomalies of the lip and/or palate that affect approximately 1/1000 live births. Their frequent occurrence as well as their extensive psychological, surgical, speech and dental involvement emphasize the importance of understanding the underlying causes. The etiology of orofacial clefts is complex, including multiple genetic and environmental factors. Rare forms, where they occur as one component of multiple congenital anomaly syndromes, have Mendelian or teratogenic origins; the non-syndromic forms of orofacial clefts are more common and are likely due to secondary gene-environment interactions. Recent advances in both molecular and quantitative approaches have begun to identify the genes responsible for the rare syndromic forms of cleft and have also identified both candidate genes and loci for the more common and complex non-syndromic variants. Animal models, in particular the mouse, have also contributed greatly to an understanding of these disorders. This review describes genes that are involved in orofacial clefts in humans and animal models and explores genetic approaches to identifying additional genes and gene-environment interactions that constitute the many factors of orofacial clefts.