Background and Objective: Enterotoxigenic Escherichia coli (ETEC) have been recognized as the most common cause of infectious diarrhea in infants and children less than five years in developing countries. The aim of the present study was to determine the frequency of ETEC isolates harboring eltB and estA genes among diarrheal children admitted to hospitals in Tabriz, Iran.Materials and Methods: In this cross sectional study, during the 7 month, a total of 450 stool samples of children younger than 5 years of age were studied. After culture and confirming, the DNA of Escherichia coli isolates were extracted by boiling method and multiplex PCR was done for detection of estA, eltB genes.Results: A total of 200 diarrheagenic E. coli strains were isolated from 450 stool samples from children with diarrhea. The prevalence of diarrheagenic E. coli isolated from stool samples was 44.44%. In order to detect eltB, estA genes simultaneously, a mixture of two primer pairs specific for the target genes was used in a single PCR. In our study, PCR assays detected 75 (37.5%) ETEC isolates. Of the ETEC strains isolated, 43 (21.5%) isolates produced heat labile toxin only, 11 (5.5%) produced heat-labile toxin and heat-stable toxin, and 21 (10.5%) produced heat stable toxin only.Conclusion: Due to the frequency distribution of enterotoxigenic isolates in Tabriz, particularly in children younger than 5 years of age, the use of molecular methods in diagnostic laboratories is recommended.