Acute upper respiratory disease in chickens is a major cause of economic losses due to high mortality rates especially in poorly managed cases. Respiratory disease in poultry is initiated by variety of viruses, bacteria and fungi. The current study aims to investigate the prevalence of avian pathogenic E. coli (APEC), their proteases and other virulence genes in respiratory viral disease outbreaks in broiler chickens. Quantitative RT-PCR (qRT-PCR) was performed on samples from 25 farms with respiratory affections, APEC was isolated and virulence determinants in E. coli were investigated phenotypically and genotypically. E. coli was isolated from different flocks (100%, n=25). They were positive to Congo red binding (100%, n=25), iss gene (100%, n=25), iutA gene (92%, n= 23), tsh gene (24%, n=6), vat gene (20%, n=5). Presence of iss gene and CR binding proves that all isolates are APEC. Although the entire 25 APEC isolates carried more than one virulence gene; either 2 genes (n=17), 3 genes (n=7) and 4 genes (n=1), no effect of the number of genes harbored on the mortality rates in different flocks was observed. The presence of two serine proteases genes (tsh and vat) was confirmed in a total of 10 isolates (40% of the isolates) with positivity to tsh gene (24%) and vat gene (20%). qRT-PCR for detection of IBV-S1, AIV-H9, AIV-H5 and velogenic NDV-F genes revealed that 96% (n=24), 44% (n=11), 12% (n=3) and 4% (n=1) of 25 farms were positive to IBV, AIV-H9, velogenic NDV and AIV-H5, respectively. The results showed that among the 25 flocks, single viral infection was observed in 12 flocks (11 IBV and 1 AIV-H9), while mixed viral infections were detected in 13 flocks; IBV/AIV-H9 (n=9), IBV/velogenic NDV (n=3) and IBV/AIV-H9/AIV-H5 (n=1).The average mortality rate was the lowest in flocks infected with IBV, higher rates of mortality were observed in flocks infected with AIV-H9, velogenic NDV and AIV-H5. Flock age seems to affect the mortality rate in flocks infected with AIV-H9 where flocks aging 16:20, 21:25 and 26:30 days suffered from 2.38%, 8.13%, 11.48% average mortality rates, respectively.