A deletion of ～20 amino acids in the stalk of the neuraminidase is frequently observed upon transmission of influenza A viruses from waterfowl to domestic poultry. A pair of recombinant H7N1 viruses bearing either a short- or long-stalk neuraminidase was genetically engineered. Inoculation of the long-stalk neuraminidase virus resulted in a higher cloacal excretion in ducks and led conversely to a lower oro-pharyngeal excretion in chickens, associated with a higher local immune response and a better survival. Therefore, a short-stalk neuraminidase is a determinant of viral adaptation and virulence in chickens, but is detrimental to virus replication and shedding in ducks.