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American white pelicans (Pelecanus erythrorhynchos) are colonial-nesting birds and their breeding sites are concentrated in a few small areas, making this species especially vulnerable to factors that can influence productivity, such as disease, disturbance, predation, weather events and loss of nesting habitat. Nearly half of the American white pelican population breeds at four colonies in the northern plains: Chase Lake National Wildlife Refuge (NWR) in North Dakota, Bitter Lake (Waubay NWR) in South Dakota, Medicine Lake NWR in Montana, and Marsh Lake in Minnesota. Thus, sustained productivity at these colonies is crucial to the health of the entire species. During the latter half of the 2002 and 2003 breeding seasons, unusually high mortality of pelican chicks was observed at these colonies. West Nile virus (WNv) was identified as one source of these losses. In 2004–2007 we monitored three major colonies in the northern plains to assess mortality of chicks during the late breeding season.We documented severe weather events, disturbance, and WNv as factors contributing to chick mortality. Before WNv arrived in the region in 2002, chick mortality after mid-July was 64%, and then jumped to as high as 44% in the years since WNv arrived. WNv kills older chicks that are no longer vulnerable to other common mortality factors (e.g., severe weather, gull predation) and typically would have survived to fledge; thus WNv appears to be an additive mortality factor. Persistence of lower productivity at American white pelican colonies in the northern plains might reduce the adult breeding population of this species in the region.