Detailed knowledge of the Hedgehog signaling pathway is fundamental to an understanding of vertebrate development as well as several birth defects in humans. Here we review various aspects of Hedgehog synthesis, secretion, distribution and function in the context of the most common anomaly of the developing forebrain in humans, holoprosencephaly. Genetic studies in numerous model organisms are beginning to elucidate the factors that are likely candidates for the causes of early embryonic defects in humans, including holoprosencephaly.