Newcastle disease virus (NDV), Infectious bronchitis virus (IBV) and avian influenza virus (AIV) are the most important respiratory viruses. Many outbreaks have been reported in Egypt in spite of the intensive use of vaccination due to the wide variations in the serotypes, the highly contagious nature, the evolution of specific tissue tropism and the mutations due to simultaneous infection of multiple virus types and use of live vaccines. In this study, 10 broiler flocks in Ismailia, Sharkeia, Gharbia, Dakahleia and Matrooh suffered of severe respiratory illness with high mortalities were examined.  A total of 138 nasal swabs and 144 tissue pools (brain, trachea, lung, liver, proventriculus, spleen, kidney, intestine and cecal tonsils) were collected from affected chickens and tested with Real Time RT-PCR (qRT-PCR) assay. Total positivity percentages of each virus in chickens were 23.46% for NDV, 18.08% for IBV and 31.20% for AIV.  Three NDV, three IBV and four AIV sequences out of 208 positive samples were selected for sequence analysis of F, S1 and M gene respectively. The sequence analysis of F gene of NDV revealed that all isolates were clustered in genotype VII and exhibited the cleavage site (¹¹²RRQKRF¹¹⁷) of virulent velogenic NDVs. The S1 gene of IBV showed that the three isolates were closely related to variant II IBV strains. The M gene sequence analysis revealed that two AI isolates belonged to H9N2 and two AI isolates belonged to H5N8 subtypes.