Inadequate dietary intake of the essential trace element selenium (Se) is thought to be a risk factor for several chronic diseases associated with oxidative stress and inflammation. Biological actions of Se occur through low-molecular weight metabolites and through selenoproteins. Several key selenoproteins including glutathione peroxidases; selenoproteins M, P, and S; and selenium-binding protein 1 have been detected in the intestine. Interestingly, Se and antioxidant selenoproteins are known to modulate differentiation and function of immune cells and contribute to avoid excessive immune responses. This review discusses the role of Se and intestinal selenoproteins in inflammatory bowel diseases, based on data from human, animal, and in vitro studies. In humans, Se deficiency is commonly observed in patients with Crohn's disease. In animal models of experimental colitis, the Se status was negatively correlated with the severity of the disease. While the cause–effect relationship of these observations remains to be clarified, the beneficial outcome of dietary Se supplementation and an optimization of selenoprotein biosynthesis in murine inflammatory bowel disease models have led to investigations of targets and actions of Se in the gastrointestinal tract. The Se status affects gene expression, signaling pathways, and cellular functions in the small and large intestine as well as the gut microbiome composition. This data, particularly from animal experiments, hold promise that adequate dietary Se supply may counteract chronic intestinal inflammation in humans.