The pathobiology of H5N1 high-pathogenicity avian influenza (HPAI) virus infection in wild waterfowl is poorly understood. This study examined the pathobiology of A/chicken/Korea/IS/06 (H5N1) HPAI in 5 migratory waterfowl species-mute swans (Cygnus olor), greylag geese (Anser anser), ruddy shelducks (Tadorna ferruginea), mandarin ducks (Aix galericulata), and mallard ducks (Anas platyrhynchos)-following intranasal inoculation or contact exposure, from which all birds became infected. In mute swans, this virus had strong vascular endothelial cell tropism, producing acute severe disease and 100% mortality; the virus was detected in various parenchymal cells; and necrotic and inflammatory changes were noted in a range of organs, including pancreas, brain, spleen, heart, oral cavity, adrenal gland, lung, and liver. The ruddy shelducks had 100% mortality, but time to death was delayed, and the lesions were primarily restricted to the brain, heart, pancreas, and spleen. The mandarin ducks had only a single mortality, with lesions similar to those in ruddy shelducks. The greylag geese became infected, developed neurological signs, and had residual meningoencephalitis when examined at termination but lacked mortality. The mallards had asymptomatic infection. These results indicate variation in the pathobiology of H5N1 virus infections in different species of wild waterfowl, ranging from severe, acute systemic disease with 100% mortality to asymptomatic infection of respiratory and gastrointestinal systems.