Background: Molecular mimicry, where foreign and self-peptides contain similar epitopes, can induce autoimmune responses. Identifying potential molecular mimics and studying their properties is key to understanding the onset of autoimmune diseases such as type 1 diabetes mellitus (T1DM). Previous work identified pairs of infectious epitopes (EINF) and T1DM epitopes (ET1D) that demonstrated sequence homology; however, structural homology was not considered. Correlating sequence homology with structural properties is important for streamlining translational investigation of potential molecular mimics. Therefore, the purpose of this work is to compare sequence homology with structural homology by calculating the structures and electrostatic potential surfaces of the epitope pairs identified in previous work from our laboratory. Results: For each epitope pair the root mean square deviation (RMSD) was calculated between their predicted structures and their electrostatic potentials were compared. Structures were predicted using the AlphaFold software program. Of the 52 epitope pairs considered here only 10 do not exhibit any matching (i.e. less than 3 residues overlap). When considering all residues the RMSD ranges from 0.33 Å to 11.66 Å with an average of 2.68 Å. Twenty-two pairs (42%) have RMSD of less than 1.5 Å and 30 (58%) less than 3 Å. Even some of the matching pairs show some electrostatic similarities that need to be considered. In general there is good agreement between the folding predicted for the isolated EINF and ET1D epitopes and the folding of the corresponding amino acid sequence in the parent antigen, but in some cases there are deviation that need to be considered, even when the RMDS is small. Conclusions: Despite differences, most of the EINF/ET1D pairs selected by sequence homology show similar structural and electrostatic distributions, indicating that the EINF may bind to the same protein targets, the major histocompatibility complex molecules, for T1DM, leading to molecular mimicry onset of the disease. These findings suggest that searching for epitope pairs using sequence homology, a much less computationally demanding approach, leads to strong candidates for molecular mimicry that should be considered for further study. Still structure and full docking calculations will be necessary to advance the in-silico molecular mimicry predictions. Here we presnt the following files: · Fasta files of all epitopes studied. · Alphafold calculated Structures of all epitopes. · Antigen structures. · Epitope pair structure comparison and their electrostatics.