Enterotoxigenic Escherichia coli (ETEC) is the most common cause of diarrhea among children. ETEC strains express colonization factors (CFs), which mediate adherence to the small intestinal epithelium and produce entrotoxins that induce diarrhea. Here, we characterized the phenotypes and genotypes of ETEC strains from 261 diarrheal stool samples from Iranian children. The prevalence of ETEC was 8.04%. Most of the isolates were positive for heat-labile and heat-stable toxins. CFA/I, CS3, CS2, and CS5 were detected from some of the clinical isolates. 33.3% of the isolates did not express CFs. The majority of ETEC isolates were identified as O127 and O128 serotypes, and 57% of the strains were resistant to more than 1 antimicrobial agent. Heat-labile enterotoxin activity was confirmed using the Y1 adrenal cell assay, rabbit ileal loop and adenylate cyclase activation tests. Regional phenotypic and genotypic characterization could help to elucidate the ecology and pathogenicity of ETEC to efficiently reduce the burden of illness brought about by ETEC. This study may lead to development of effective prophylactic measures.