Background: Many diseases create the cytolethal-distending toxin (CDT), which is representative of an emerging family of recently identified bacterial compounds. Objective: This study was performed to detect the antibiotic resistance properties and distribution of cdtB and clbA in E. coli strains isolated from urine and stool samples.  Materials and Methods: The sensitivity test was evaluated by using different types of antibiotics in the current study, and the cdtB and clb genes were detected by PCR in all bacterial isolates. Results: The antibiotics sensitivity test show variable degrees of sensitivity and resistance. The high percentage of sensitivity was achieved against amikacin at a percentage of 86% and ciprofloxacin, ceftazidime, gentamicin, and tobramycin at a percentage of 80%, whereas trimethoprim and aztreonam at 64% and 60% respectively. In this study, most isolates were resistant to amoxicillin (92%); while showing different degrees of resistance against other types of antibiotics ranging from tetracycline (62%) to amikacin 4%.  The frequency of MDR bacteria was about 64 % (32 isolates), 30 from urine, and 2 others from stool. The results showed that the clbA gene was found in 6 bacterial isolates (12%), whereas the other 44 (88%) isolates don't have this gene, while the cdtB gene wasn't found in any one of the bacterial isolates. Conclusions: E.coli was recorded as multidrug resistance (MDR) and the clb gene was found only in 6 bacterial isolates but it was not the cdtB gene detected in all isolates.