Background: Some of the pathogenic strain of Escherichia coli (E. coli) can cause none-enteritidis and enteritidis diseases. Antibiotic resistance is important in treatment of infectious diseases. The aim of this study was assessment of the the frequency of antibiotic-resistance genes in the clinically isolated enteroaggregative and enteropathogenic virutypes of Escherichia coli (EPEC and EAEC).Methods: Clinically isolated strains were identified using biochemical test and antibiotic sensitivity assessment performed by disc diffusion method according to Clinical and Laboratory Standards Institute (CLSI) guidelines, and epsilometer test (E-test) in different groups. The virutypes genes were identified via multiplex polymerase chain reaction (M-PCR).Findings: All of the clinically isolated strains (100%) were resistance to erythromycin and 93.33% to ampicillin; 66.66% of the strains were susceptible to gentamycin and 60.00% to ciprofloxacin. Many of strains were multiple-drug resistant (MDR). In multiplex polymerase chain reaction, an enteroaggregative virutype of Escherichia coli was isolated (2%) carrying gene CVD432.Conclusion: There is a serious risk for patients due the importance of Escherichia coli as major cause of child diarrhea in developing countries and according to increasing in utilization of resistance to the antibacterial drugs. Inconsistency in our finding and other researches may be due the difference sources of isolation sites; in this study, isolated sources were from urine samples, but in other researches, fecus was the source. Another source of inconsistency may lay in geographical differences.