The interactions we have described enable the intestine to respond appropriately to antigenic challenge in an effective and coordinated way. This is of vital importance when one considers the dual role of the intestine as a first line of defence against harmful microorganisms and as the route by which the animal obtains nutrition. Under normal circumstances, these interactions select for an appropriate cell phenotype by providing a network of interactions that contribute to intestinal homeostasis. If there is dysfunction of any component, then other cells will be affected. For example, if down-regulation of the mucosal immune response is not effective, damage to the epithelium, nerves and muscle may occur during an inflammatory response. Similarly, if the integrity of the epithelium is disrupted, damage to the elements of the mucosal immune system may occur. This model would suggest that these interactions must be considered if one wishes to adequately explain diseases such as IBD and design innovative therapeutic regimens. Future interdisciplinary research will shed light on the web of interactions occurring in the intestinal environment and provide a novel view of the respective contributions of the immune system and its local environment to cell differentiation, function and regulation.