A structural analysis was conducted of peptides responsible for inducing celiac disease, as well as of the structural fragments they are located in, i.e. the so-called “extended structural motifs”. These motifs originated from wheat A-gliadin and constituted a standard for the analysis of the other proteins. Experiments were carried out based on in silico methods. Analyses covered a total of 403 sequences of selected cereal and seed proteins. Of all the analysed sequences, 155 were found to contain tetrapeptides (potentially known as toxic for celiac disease), namely: QQQP, QQPY, PSQQ, QPYP, including 29 proteins in which the tetrapeptides were constituents of a structural motif with a longer sequence. These were proteins of wheat, barley and oat. All the extended motifs occurred in a hydrophilic surrounding, attaining the structure of beta-turn and random coil. Computer-aided design of the proteolysis process of selected proteins was carried out as well in the aspect of celiac-toxic peptide release. Active fragments were released from twenty-eight proteins by thermolysin, K proteinase and prolyl oligopeptidase.