Atypical enteropathogenic Escherichia coli (aEPEC) have emerged as a significant cause of pediatric diarrhea worldwide. Due to the absence of BFP fimbriae (bundle-forming pili), aEPEC are unable to develop the 3 h-localized adhesion pattern observed in typical EPEC. Since some aEPEC show the adherence phenotype observed for other pathotypes of E. coli, the aim of this study was to investigate, in aEPEC, the presence of adhesin genes found in other pathogenic E. coli and to analyze, by comparative proteomic analyses, the protein extracts isolated from aEPEC BA320 (localized-like), Ec292/84 (aggregative) and 9100-83 (diffuse) and BA4013 (non-adherent). Initially, transmission electron microscopy demonstrated the presence of different filamentous structures anchored to the surface in the four EPEC isolates. PCR analyses of aEPEC revealed the presence of the genes fimA, fimH, papA, ecpA, ldaH, pilS, daaC, sfpA, lpfA O113 and polymorphic variants (lpfA1 and lpfA2), which are also present in other pathotypes of E. coli. On the other hand, proteomic analyses of aEPEC extracts obtained with an Omnimixer and precipitated with ammonium sulfate, using 2D gel electrophoresis and LC-MS/MS, identified several proteins involved in different functional processes of bacteria, including proteins involved in the mechanism of bacterial adhesion, namely: a histone-like nucleoid structuring protein (H-NS), an outer membrane protein (OmpX), universal stress proteins (Usp), L-fucose mutarotase (FucU) and galactose-binding transport protein (MglB) associated with the action of adhesins of E. coli fimbriae. The protein extract also revealed "hypothetical" proteins, particularly a putative filamentous protein found in aEPEC with the phenotypes of localized-like, diffuse and aggregative adherence. Therefore, we conclude that the genes encoding type 1 fimbriae and ECP fimbriae are highly prevalent in aEPEC isolates, and that the proteins identified in the proteome of four aEPEC strains, which are related to different bacterial functions, can operate as protein complexes, directly or indirectly involved in adhesion processes.