We approached the problem of genotyping influenza A viruses by analyzing each gene segment independently, segregating gene segments into subtypes and subsequently into lineages. The genotype of an influenza A viral strain is the sequential aggregate of the eight assigned gene segment lineages. A nomenclature for influenza A viral genotypes will allow researchers to unequivocally describe influenza A viral genotypes to analyze, compare and communicate the molecular epidemiology of the virus. In this report, we define a nomenclature for influenza A viral genotypes and describe a web tool developed for genotyping influenza A viruses from genome sequences. Our tool facilitates identification of reassortment events between divergent lineages.