Background: Antibiotic resistance is widespread among diarrheagenic Escherichia coli in developing countries, where the overuse of antibiotics is common. Information regarding β-lactamases, especially Extended-Spectrum β-Lactamases (ESBLs) in diarrheagenic pathogens should be considered in clinical management when an optimal treatment is needed. Objectives: The main objective of this study was to investigate the prevalence of bla_CTX-M, bla_SHV and bla_TEM β-lactamase genes among enteropathogenic E. coli (EPEC) isolates in Tehran, Iran. Materials and Methods: Stool specimens were collected from children with diarrhea during a 17-month period from 2011 to 2013. Routine biochemical tests were performed for identification of E. coli isolates. The isolates were further examined by PCR for the presence of eae, stx1, stx2 and bfp genes. EPEC isolates have been screened for different β-lactamase genes. Genotyping EPEC isolates harboring bla_CTX-M15 gene was performed through Multi-Locus VNTR Analysis (MLVA). Results: Of 42 EPEC, eight isolates carried the bla_CTX-M1. None of the isolates carried bla_CTX-M2 and bla_CTX-M9. The bla_CTX-M15 variant was identified in all of bla_CTX-M1-positive isolates. Furthermore, bla_SHV and bla_TEM genes were detected in 40.5% (n = 17) and 19% (n = 8) of all EPEC isolates, respectively. No significant association was observed between the existence of bfp gene and presence of those β-lactamase genes (P > 0.05). MLVA analysis revealed high genetic diversity among bla_CTX-M15-positive isolates. Conclusions: Our study emphasized the increasing role of ESBL genes, especially bla_CTX-M15 in EPEC isolates. Keywords: Enteropathogenic Escherichia coli; Strains; Diarrhea