Molecular mimicry occurs when foreign- and self-peptides contain similar epitopes that may lead to autoimmune responses in susceptible individuals. Identifying molecular mimics and studying their properties is key to understanding onset of autoimmune diseases such as type 1 diabetes mellitus. Previous work identified, catalogued, and indexed 61 pairs of infectious epitopes (EINF) and type 1 diabetes epitopes (ET1D) that show sequence homology. Of these 61 pairs, 35 were conserved among different pathogenic species. However, the previous study only assessed sequence homology and did not consider structural homology. The purpose of this work was to analyze the structures and electrostatic potentials of the 35 pairs of epitopes. To accomplish this, we calculated the root mean square deviation (RMSD) between predicted structures, electrostatics, and hydrophobicity of each pair of epitopes. Structures were predicted using the AlphaFold and I-TASSER suites provided by the University of Utah’s Center for High Performance Computing (CHPC). Successful structurally matched EINF and ET1D pairs yielded RMSD of < 1.5 Å, of which AlphaFold found a 76.5% success rate and I-TASSER, 82.35%. Of the pairs that could not be structurally matched (< 3 residues aligned), AlphaFold found four unique pairs, and I-TASSER found two unique pairs. Therefore, both AlphaFold and I-TASSER agreed on four EINF/ET1D structurally unmatched pairs. Despite structural differences, these four EINF/ET1D pairs show similar electrostatic distributions, indicating that they may still bind to the same protein targets (MHC molecules) for type 1 diabetes. This shows that finding epitope pairs using a less computationally demanding approach leads to very good candidates for further study.