Seven commercial layer flocks with lesions suggestive of respiratory and reproductive problems were investigated during the study period (one year) of January to December 2016. The study comprised of necropsy, incidence, farm wise mortality, gross and histopathological lesions, detection of LPAI (H9N2) virus by RT-PCR, isolation of E. coli and detection of virulence genes associated with E. coli by PCR. Studies on the farm incidence and mortality due to LPAI among seven-layer farms showed an average mortality rate of 3.03% ranging between 1.04 to 18.75%. Gross and microscopic lesions were predominantly found in organs of respiratory and reproductive tracts. All the 52 samples from seven flocks tested for the presence of LPAI (H9N2) virus were found positive. Out of the 52 tissue samples processed for bacterial isolation, 40 samples (76.92%) were found positive for secondary E. coli infection.