The recent identification of some of the human holoprosencephaly genes is beginning to elucidate the intricate developmental programs that pattern normal and abnormal brain development. Here we present some of these advances in the context of our present understanding and conclude with some speculations regarding the direction for future investigations. We are living in a tremendously exciting time in medicine with the rapid application of molecular genetic approaches to the understanding of human disease. It is the purpose of this review to stress the underlying principals of our approach at a level that can be readily appreciated by colleagues who themselves are experts in brain anatomy but not necessarily the molecular genetics of brain development.