The cornerstone of treatment of coeliac disease is a gluten-free diet devoid of proteins from wheat, rye, barley and related cereals. Oats are tolerated by most patients with coeliac disease but are not totally innocent. There are considerable differences between individual patients with respect to clinical and mucosal responses to gluten challenge. In vitro and in vivo testing has identified synthetic peptides that are toxic to the coeliac small intestinal mucosa. This toxicity overlaps at least partly to the known epitopes that are recognised by small intestinal T-cells. However, the clinical significance of several of these epitopes is unclear, as is the maximum level of gluten intake that can be recommended to be safe for patients with coeliac disease. Future efforts may lead to better understanding of the disease processes as well as possible new therapeutic options.