Celiac disease (CeD) is an autoimmune disorder triggered by gluten proteins, affecting approximately 1 % of the global population. The 33‐mer deamidated gliadin peptide (DGP) is a metabolically modified wheat‐gluten superantigen for CeD. Here, we demonstrate that the 33‐mer DGP spontaneously assembles into oligomers with a diameter of approximately 24 nm. The 33‐mer DGP oligomers present two main secondary structural motifs–a major polyproline II helix and a minor β‐sheet structure. Importantly, in the presence of 33‐mer DGP oligomers, there is a statistically significant increase in the permeability in the gut epithelial cell model Caco‐2, accompanied by the redistribution of zonula occludens‐1, a master tight junction protein. These findings provide novel molecular and supramolecular insights into the impact of 33‐mer DGP in CeD and highlight the relevance of gliadin peptide oligomerization.