In this study, 50 vaccinated broiler and one layer flock from Beni-Suef, Fayoum and Minia governorates were investigated. Necropsy lesions were suggestive of LPAI-H9N2 or NDV. Samples of tracheal swabs and organs were subjected for viral isolation and molecular characterization. Specific RT-PCR for the NDV F-gene and the HA gene of the LPAI-H9N2 viruses was used. Virus isolation and primary identification using HI test revealed 37.5 and 43.3-46.2% prevalence for LPAI-H9N2 and NDV viruses, respectively. Phylogenetic analysis of partial sequences of the F gene showed that NDV viruses belong to genotype II and VII-1.1. as indicated by the F0 protein proteolytic cleavage site motifs (aa112-117) of the NDV strains F-gene. The vNDV isolates were 98.7-99.3% and 96.6-98.9% identical to each other based on nucleotide and amino acid identities, respectively. Compared to their counterpart isolates; the lentogenic strains shared 98-99.2% and 96.3-98.1% nucleotide and amino acid identities to the LaSota reference strain. The LPAI-H9N2 phylogeny of the HA gene showed that the 2 isolates obtained in this study are related to each other and related to recent 2016-2018 Egyptian H9N2 strains. Notably, the 2 strains showed higher identity (≥99%) to recent Israeli 2018 isolates with several amino acid changes. The current study revealed wide spread of both NDV and LPAI-H9N2 viruses. The vaccine failure and the mismatch between the vaccine and circulating NDV viruses is the most probable cause of current outbreaks. The LPAI-H9N2 viruses are divergent form their ancestral viruses in Egypt indicating continuous circulation and vaccine pressure induced mutations