The intestinal epithelium represents one of our most important interfaces with the external environment. It must remain tightly balanced to allow nutrient absorption, but maintain barrier function and immune homoeostasis, a failure of which results in chronic infection or debilitating inflammatory bowel disease (IBD). The intestinal epithelium mainly consists of absorptive enterocytes and secretory goblet and Paneth cells and has recently come to light as being an essential modulator of immunity as opposed to a simple passive barrier. Each epithelial sub-type can produce specific immune modulating factors, driving innate immunity to pathogens as well as preventing autoimmunity. The enteroendocrine cells comprise just 1% of this epithelium, but collectively form the bodies' largest endocrine system. The mechanisms of enteroendocrine cell peptide secretion during feeding, metabolism and nutrient absorption are well studied; but their potential interactions with the enriched numbers of surrounding immune cells remain largely unexplored. This review focuses on alterations in enteroendocrine cell number and peptide secretion during inflammation and disease, highlighting the few in depth studies which have attempted to dissect the immune driven mechanisms that drive these phenomena. Moreover, the emerging potential of enteroendocrine cells acting as innate sensors of intestinal perturbation and secreting peptides to directly orchestrate immune cell function will be proposed. In summary, the data generated from these studies have begun to unravel a complex cross-talk between immune and enteroendocrine cells, highlighting the emerging immunoendocrine axis as a potential target for therapeutic strategies for infections and inflammatory disorders of the intestine.