Highly pathogenic (HP) avian influenza viruses (AIV) present an ongoing threat to the world poultry industry. In order to develop new AIV control strategies it is necessary to understand the underlying mechanism of viral infection at mucosal respiratory sites. Chicken and duck tracheal epithelial cells systems (TEC) were developed to study early host responses to AIV infection on TEC. Infection of 2 week-old chickens and ducks with the highly pathogenic AIV H5N1 Ck/Hong Kong/220/97 and Egret/Hong Kong/757.2/02 viruses together with TEC early responses to infection suggest the induction of differential innate immune responses. Growth curves indicated that although chicken and ducks TEC supported viral replication and re-infection, the capacity of the two viruses to replicate was not equal. A 42K probes chicken microarray system used to characterize differences in gene expression between chicken tracheal epithelial cells infected with these two highly pathogenic AIV identified expression of virus-specific molecular markers. The existence of dissimilar patterns of host gene expression as early as six hours post infection suggests that the differential growth characteristics of the two highly pathogenic AIV in tracheal epithelial cells is preceded by distinct host responses.