For a better understanding of evolution of influenza viruses, a chicken-origin and wild-bird-origin low-pathogenic avian influenza virus (LPAI) was serially passaged in chickens. Sequences of the hemagglutinin (HA) and neuraminidase (NA) genes at each passage level were compared to those of the parental virus. Multiple mutations occurring early during passage were detected, but these were maintained during passages. Interestingly, a number of the observed mutations already existed in the parental virus, as indicated by the presence of single-nucleotide polymorphisms. The greatest numbers of mutations occurred during passage of wild-bird-origin LPAI, where a 20-amino-acid deletion in the NA gene that was observed during the first passage was maintained during subsequent passages. Subsequent experiments showed that this NA deletion was already present as a minority population in the parental virus. These results showed that a selection process favoring a viral subpopulation had occurred.