A total of two hundred diseased Saso chicks with omphalitis were examined (1400 samples) for the isolation of E. coli from different organs (liver, ceacum, spleen, heart, lung, yolk sac and cloacal swab).Results showed that 64 cases were positive with an incidence of 32%. Fifty isolates (25%) of E.coli were recovered from chicks could be serogrouped in 19 O groups with the most predominant serotype was O91 20 % (10 out of 50 isolates), O26 10% (5 strains out of 50) O788% (4 strains out of 50), and 7 strains untypable E. coli 14%. Among E. coli O groups were found to be resistant to Amoxicillin 93.02% followed by Tetracycline 74.42%, Enrofloxacin 46.51%, Erythromycin 30.32%, Ciprofloxacin 27.91%, Norofloxacin and Streptomycin 20.93% and Gentamycin 6.98%. While they were found to be sensitive for Gentamycin, Streptomycin, Ciprofloxacin, Tetracycline, Erythromycin, Norofloxacin, Enrofloxacin, and Amoxicillin as the following: 88.37%, 46. 51%, 34.89%, 23.26%, 18.60%, 9.30%, 9.30% and 6.98%, respectively. The incidence rate of eaeA gene of E.coli was 15.79%.Quaternnary ammonium compound (qacEΔ1) gene also was detected in E. coli with incidence rate 63.16%. Keywords: Omphalitis, E. coli, Virulence gene, Antibiotic resistance, Disinfectant resistant gene