In conclusion, our results reveal the active circulation of two different APV genotypes in house sparrows from Spain, with variable prevalence between age classes. In addition, our results confirm that visual inspection and molecular testing of lesions provide an incomplete estimate of APV circulation in house sparrow populations. First, the minimally invasive sampling methods employed in this study of live wild birds can involve a percentage of false negatives. Whilst the skin lesions had a characteristic appearance consistent with avian pox in this species, PCR was only able to detect avian poxvirus DNA in 63% of cases. Moreover individuals which display clinical signs of disease may not represent all individuals with current infection, nor do they capture complete information on historic infection. Further studies of seroprevalence would be extremely useful for obtaining an estimate of the real exposure to this virus in wild bird populations.