Surveillance on Avian Influenza Virus in Egypt during 2012 -2013 was undertaken to update the epidemiology of avian influenza virus infections among poultry flocks in Egypt. A total of 148 commercial chicken farms were tested by single-plex RT-PCR for direct detection of avian influenza viruses using type A specific nucleoprotein (NP) gene primer sets. The results revealed 5 positive chicken flocks infected with type-A AIV. These viruses were successfully isolated and propagated in SPF eggs. H5N1/HI test was positive only for three chicken flocks. Subtype specific (RT-PCR) revealed 3 positive H5 chicken flocks (2%) and 2 positive H9 chicken flocks (1.35%). All examined chicken flocks were negative for H7 subtype. Multiplex RT-PCR using H5, H7 and H9 subtypes specific primers confirmed these results. This shows the continuous co-circulation of the AIV H5 and H9 in commercial chicken flocks in Egypt complicating the respiratory problems in affected flocks. Egypt between 2012 -2013. Swabs were placed in 1-2 ml isotonic phosphate buffered saline (PBS) PH 7.0-7.4, chilled immediately on frozen gel packs and submitted to the laboratory as quickly as possible.Tracheal and cloacal swabs collected from each commercial poultry flock were pooled separately. Tracheal swabs were screened with RT-PCR for AIV detection, but cloacal swabs in PBS with antibiotics were subjected for virus isolation. AntiserumSpecific polyclonal antiserum against avian influenza subtype H5N1 was obtained from X-OVO (flock screen, Batch: 1/09) produced by OIE/FAO and National