AbstractHoloprosencephaly (HPE) is a malformation of the human brain caused primarily by incomplete division of the prosencephalon into two halves and is often associated with various facial anomalies. Although HPE is rather rare in newborns (1/10,000–15,000 births), it is frequently encountered in therapeutic abortuses (>1/250). To date, nine gene mutations responsible for human HPE have been identified, but the pathogenetic mechanisms of the craniofacial anomalies in HPE have just begun to be understood. Here, we summarize our studies on human embryos with HPE and discuss the embryogenesis and the underlying molecular mechanisms of HPE malformations under the following headings: pathology, pathogenesis, and critical period of development. © 2007 Wiley‐Liss, Inc.