Advances in developmental biology combined with progress in human genetics are helping us decipher how the craniofacial region develops and how the consequences of misdirected development result in malformation. This review describes the molecular etiology of a number of craniofacial developmental anomalies. The more common craniofacial anomalies cleft lip and palate and craniosynostosis, as well as cleidocranial dysplasia, hemifacial microsomia, holoprosencephaly, enlarged parietal foramina, Treacher Collins syndrome and cherubism are discussed.