The emergence and spread of H5N1 avian influenza viruses from Asia through to Europe and Africa pose a significant animal disease problem and have raised concerns that the virus may pose a pandemic threat to humans. The epizootological factors that have influenced the wide distribution of the virus are complex, and the variety of viruses currently circulating reflects these factors. Sequence analysis of the virus genes sheds light on the H5N1 virus evolution during its emergence and spread, but the degree of virus variation at the level of an individual infected bird has been described in only a few studies. Here, we describe some results of a study in which turkeys, ducks and chickens were infected with either one of two H5N1 or one of three H7N1 viruses, and the degree of sequence variation within an individual infected avian host was examined. We developed 'deep amplicon' sequence analysis for this work, and the methods and results provide a background framework for application to disease outbreaks in the field.