Analysis of the structure of the avian influenza (AI) virus hemagglutinin (HA) gene and protein has yielded a wealth of information on the virulence mechanisms of influenza viruses. The AI hemagglutinin appears to be unique in its capacity to accept basic amino acids at its proteolytic cleavage site (PCS). The association of multiple basic (MB) amino acids, HA cleavage, tissue spread and virulence by AI strains first proposed in the late 1970s and early 1980s [Klenk, H.D., Rott, R., Orlich, M., 1977. J. Gen. Virol. 36, 151-161; Bosch, F.X., Garten, W., Klenk, H.D., Rott, R., 1981. Virology 113, 725-735] has held fast for two decades now. While other structural characteristics and other genes can certainly influence virulence, the presence of 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. The recent outbreaks of highly pathogenic AI in Mexico, Australia, Pakistan, Hong Kong and in the ongoing outbreak of moderately pathogenic H7 avian influenza in the northeast US have all provided new and useful information regarding the role of HA RNA and protein structure in both virulence and host adaptation. 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.