We examined whooper swans naturally infected with avian influenza virus (H5N1) to evaluate the possible zoonotic risk of swan feathers. Viruses were isolated from feather calami. Immunohistochemical testing revealed that virus antigens were present in the feather epidermis and feather follicle wall epidermis of some feathers. RT-PCR and genetic sequencing using paraffin sections of swan feathers confirmed the presence of avian influenza virus (H5N1) in the feather tissue. These results indicate that the feathers could have the risk for zoonotic infection from infected wild swans.