Technical Abstract: Analysis of the structure of the avian influenza (AI) virus hemagglutinin (HA) gene yields a wealth of information on the virulence mechanisms of influenza viruses. The AI hemagglutinin is unique in its capacity to accept basic amino acids at its' proteolytic cleavage site (PCS). Other structural characteristics and other genes can certainly influence virulence, the presence of the MB amino acids at the PCS has provided a hallmark structural feature which justifies continuing sequence analysis of emerging field isolates of AI strains. In addition to this structural feature, the distal tip of the HA is prone to appearance and disappearance of glycosylation sites, some of which have been associated with virulence. We have previously noted that stable RNA secondary structure near the PCS is related to the acquisition of virulence and have proposed that the secondary structure may promote the insertion of basic amino acids. In this report we evaluate the phylogenetic relationships for three recent isolates of highly pathogenic avian influenza viruses and the possible virulence factors associated with their primary and secondary structure.