Coeliac disease is a complex inflammatory disorder of the small intestine, induced by dietary gluten in genetically susceptible individuals. Recently, the nature of gluten-derived peptides recognized by gut-derived T cells from patients has been elucidated. It has further been established that the binding of such peptides to HLA-DQ2 and DQ8 molecules is enhanced following the modification of the peptides by the ubiquitous enzyme tissue transglutaminase. This knowledge has allowed the establishment of a molecular basis for the well-known association between coeliac disease and the expression of these HLA-molecules. This article summarizes the latest progress in coeliac disease molecular biology.