The spread of H5N1 avian influenza viruses (AIV) from China to Europe has raised significant global concern about their potential to infect humans and cause a pandemic. In spite of their significant threat to human health, remarkably little AIV whole genome information is available. We report here a preliminary analysis of the first large-scale sequencing of AIV including 2,196 AIV genes and 169 complete genomes. We combine this new information with public AIV data to identify new gene alleles, persistent genotypes, compensatory mutations, and a potential virulence determinant.