Crohn's disease and ulcerative colitis, collectively known as inflammatory bowel disease (IBD), are chronic, recurring, inflammatory conditions of the intestine. The precise mechanisms underlying the pathogenesis of IBD are not yet clear but they are believed to involve a number of precipitating factors, most notably genetic susceptibility and environmental influences. The autonomic nervous system (ANS) has long been known as a critical regulator of intestinal function and much evidence now exists to suggest that it also plays an important role in the development of IBD. Dramatic changes in the ANS in IBD are apparent from the cellular to the molecular level ultimately leading to altered communication between the ANS and effector cells of the intestine. This review aims to synthesize the current understanding of the pathogenesis of IBD with a particular emphasis on the role that the ANS plays in the progression of these diseases.