This article reports a full-term infant with Hirschsprung disease (HD) who was diagnosed to have hypertrophic pyloric stenosis (HPS) and agenesis of corpus callosum (ACC). Pyloric stenosis is known to be associated with HD. To our knowledge, the combination of Hirschsprung disease, hypertrophic pyloric stenosis and agenesis of corpus callosum has not been reported previously. We believe these three conditions are due to an underlying pathophysiologic mechanism.