The gut has the capacity to function as an autonomous organ. However, in normal conditions, the gut and the central nervous system talk to each other through the autonomic nervous system (ANS), represented by the sympathetic (i.e. the splanchnic nerves) and the parasympathetic nervous system (i.e. the vagus nerve and the sacral parasympathetic pelvic nerves). The brain is able to integrate inputs coming from the digestive tract inside a central autonomic network organized around the hypothalamus, limbic system and cerebral cortex and in return to modify the ANS and the hypothalamic pituitary adrenal axis (HPA axis). An abnormal functioning of these brain-gut interactions has been described in irritable bowel syndrome (IBS) classically considered as a biopsychosocial model where stress plays a promoting role. Inflammatory bowel diseases (IBD) result from an inappropriate inflammatory response to intestinal microbes in a genetically susceptible host. In this article we review the current knowledge on the possible involvement of a dysfunction of brain-gut interactions in the pathogeny of IBD as represented by a dysfunction of the ANS, an abnormal HPA axis and cholinergic anti-inflammatory pathway, a deleterious effect of stress and depression as well as an abnormal coupling of the prefrontal cortex-amygdala complex and an abnormal relation between the microbiota and the brain as pro-inflammatory factors. Therapeutic approaches with the aim to restore an equilibrium of these brain-gut interactions are of interest.