Celiac Disease (CeD) is a highly prevalent chronic immune-mediated enteropathy developed in genetically predisposed individuals after ingestion of a group of wheat proteins (called gliadins and glutenins). The 13mer α-gliadin peptide, p31-43, induces proinflammatory responses, observed by in vitro assays and animal models, that may contribute to innate immune mechanisms of CeD pathogenesis. Since a cellular receptor for p31-43 has not been identified, this raises the question of whether this peptide could mediate different biological effects. In this work, we aimed to characterize the p31-43 secondary structure by different biophysical and in silico techniques. By Dynamic Light Scattering (DLS) and using an oligomer/fibril-sensitive fluorescent probe, we showed the presence of oligomers of this peptide in solution. Furthermore, Atomic Force Microscopy (AFM) analysis showed p31-43 oligomers with different height distribution. Also, peptide concentration had a very strong influence on peptide self-organization process. Oligomers gradually increased their size at lower concentration. Whereas, at higher ones, oligomers increased their complexity, forming branched structures. By Circular Dichroism, we observed that p31-43 self-organized in a poly-proline II conformation in equilibrium with β-sheets-like structures, whose pH remained stable in the range of 3 to 8. In addition, these findings were supported by Molecular Dynamics Simulation. The formation of p31-43 nanostructures with increased β-sheet structure may help to explain the molecular etiopathogenesis in the induction of pro-inflammatory effects and subsequent damage at the intestinal mucosa in CeD.