The present study identified virulence genes and pathological changes caused by Escherichia coli in chicken carcasses condemned for airsacculitis and assessed if the histopathological examination and polymerase chain reaction (PCR) were effective for studies like this. Trachea, liver, and lung were collected from 30 chickens with suspected airsacculitis that has been condemned in the inspection line. The samples were analyzed by PCR to simultaneously identify two virulence genes (iss and tsh genes) and for histopathological testing. PCR efficiently genotypically characterize the E. coli isolates, where the virulence genes iss and tsh were found in three birds simultaneously. The histopathological examination detected a predominance of heterophils and mononuclear cells in the trachea (100%), lung (90%), and liver (13.3%). The liver was the organ where practically no alteration was diagnosed. The results of multiplex PCR for the tsh and iss virulence genes indicate the great potential of the approach in the characterization of E. coli isolates. Unspecific identification did not occur, thus making it necessary to use technologies for the identification and prevention of this agent in aviaries and poultry abattoirs.