Holoprosencephaly is a malformation of the cerebral hemispheres resulting in the absence of the inter-hemispheric fissure along with other defects of brain development. Frequently midline defects of the craniofacial structures are also present. This malformation sequence has been of interest for many years because of the well recognized genetic and environmental pathogeneses, although the molecular pathogenesis remained elusive. Recent studies have begun clarifying the molecular pathogenesis of holoprosencephaly. Herein is reviewed the syndromes associated with holoprosencephaly, the pathology of this disorder, genetic and environment factors, and a current understanding of the molecular pathogenesis of this disorder.