Holoprosencephaly (HPE) is one of the major brain anomalies caused by the failure of cleavage of the prosencephalon during the early stage of development. Over 200 cases of HPE in the Kyoto Collection of Human Embryos were observed grossly and histologically, with special emphasis on the anomalies of the brain, face and eye. The facial anomalies of HPE human embryos after Carnegie stage (CS) 18 could be classified into cyclopia, synophthalmia, ethmocephaly, cebocephaly, and premaxillary agenesis, similarly as the classical classification for postnatal cases. On the other hand, HPE embryos at CS 13-17 showed some characteristic facies which are different from those in older embryos. In the present paper, pathology and phenotypic variability in HPE embryos were discussed from the embryopathological point of view. Recently, the molecular mechanism of HPE has been clarified by the techniques of gene manipulation, and various HPE genes have been identified by gene analysis of familial HPE cases. HPE is one of the major CNS anomalies which have been extensively studied and provides a clue to the mechanisms of normal and abnormal development of craniofacial structures.