Abstract: Background: Avian pathogenic E. coli cause serious disease in chickens, which mainly chracterised by airsaculitis, perihepatitis and pericarditis resulting in large economic losses in poultry industry worldwide. Methodology: In order to investigate the genetic variation among different E. coli strains isolated from chickens, one hundred diseased broiler chickens at Sharkia province, Egypt were examined. Liver and heart blood samples were collected from each bird and subjected to bacteriological examination, where the prevalence of E. coli was 60% from the total collected samples. Escherichia coli strains were serogrouped. The PCR was used for detection of Shiga-like toxins genes (stx1 and stx2), attaching and effacing (eaeA) gene and enterohaemolysin gene (hly) in the typable isolated E. coli strains. Results: The results showed that the isolated strains belonged to 11 serogroups including O1, O2, O26, O44, O55, O78, O111, O119, O125, O127 and O128. Untypable strains were also recovered. The detected virulence genes were stx1 in all E. coli strains (100%), stx2 in 17 strains (47.2%), eaeA in 12 strains (33.3%) and hly only in three strains (8.3%). Conclusion: In conclusion, the combination of genotypic and phenotypic analysis of E. coli is more valuable as an epidemiological tool for identification of isolates. This study established the presence of stx1 and stx2 containing E. coli in chickens.