Hedgehog (Hh) proteins are members of a family of secreted signalling factors that orchestrate the development of many organs and tissues including those of the gastrointestinal (GI) tract. The requirement for Hh activity is not limited to early development but underlies the homeostsasis of a number of tissues and abnormal activity of the Hh pathway is associated with several GI malignancies. Understanding the roles and mechanisms of action of Hh signalling both in development and post-natally should thus give novel insights into potential treatments for these diseases. Here we focus on the Hh signalling pathway and its role in GI tract development and maintenance, and consider the diseases resulting from aberrant Hh activity.