Non-syndromic orofacial clefts and tooth agenesis are two of the most common craniofacial birth defects. Both of them have a complex etiology, with genetic and environmental factors involved. Additionally, the epigenetic modifications have been implicated in the pathogenesis of these structural malformations. Despite an increasing number of research studies, using a variety of methodological approaches, the role of genetic factors in the etiology of orofacial clefts and tooth agenesis is still not well elucidated. The most consistent findings across studies concerning the genetic factors influencing the risk to orofacial clefts include the association of polymorphic variants of the IRF6 gene and the chromosomal locus 8q24.21. The major candidate gene for tooth agenesis in the European populations is WNT10A; its pathogenic mutations are present in more than 50% of patients with this dental anomaly. It has been found that both orofacial clefts and tooth agenesis, which co-occurrence is often reported, may share common candidate genes.