The intestine is a rich venue for interactions between the neuroendocrine and immune systems. Functional regulation of mucosal immune responses can be exerted through local neuroendocrine paths by neuropeptides from the neurons of the enteric nervous system and peptide hormones. Immune regulation can also be exerted through influences in the central nervous system activating the hypothalamic-pituitary-adrenal axis, and through the activation of the autonomic nervous system. The integrity of these systems can alter the outcome of immune-mediated inflammation in the gut. The role of these pathways in the regulation of cytokines is examined, and the implications for Crohn's disease and ulcerative colitis are explored.