Composting poultry mortality and farm wastes infected with mixed respiratory infection viruses one of major goals for control and combating this infection. To achieve fair level of biosecurity protocol in poultry farms infected with virus induced mortality, proper hygienic disposing is imperative from socioeconomic and health risk concept. Collected fresh dead birds, their litter and wastes from commercial flocks with high mortalities associated with mixed respiratory symptoms were subjected to composting process. Molecular characterization of avian influenza virus (H9N2) and Newcastle disease virus (H9N2 & NDV) were recorded from cecal tonsils and trachea respectively of morbid and dead chickens before subjecting to composting. Characterization was done by Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) using specific primers targeting the matrix (M) gene, H9 gene of AIVs and fusion (F) gene of NDV were used. The (HA) hemagglutinin glycoprotein gene of H9N2 isolates were partially amplified by RT-PCR, directly sequenced. The nucleotide and amino acid sequence analysis of the hemagglutinin gene of the characterized Egyptian viruses showed the highest similarity with one group of recent Israeli circulating strains. The Phylogenetic analysis for HA gene of H9 AIV showed the placement of the Egyptian viruses within the same lineage of H9N2 viruses that circulated in the region from 2006 especially with recent Israeli strains of G1 lineage (group B). Failure of re-characterization of AIV (H9N2) and NDV in the current work on day 15^th of composting treatment confirmed the efficacy of composting poultry farm mortalities and wastes. Composting in closed vessel (newly designed closed copmposter) achieved proper secure microbial activity that inactivated H9N2 AIV and NDV viruses via increased temperature and decreased moisture content of composting poultry mortality and farms wastes with no isolation and characterization of these viruses. The product suggested to be used for agronomic activities.