Scientists have feared that emerging infectious diseases could complicate efforts to conserve rare and endangered species, but quantifying impacts has proven difficult until now. We report unexpected impacts of West Nile virus (WNv) on radio-marked greater sage-grouse (Centrocercus urophasianus), a species that has declined 45–80% and is endangered in Canada and under current consideration for federal listing in the US. We show that WNv reduced late-summer survival an average of 25% in four radio-marked populations in the western US and Canada. Serum from 112 sage-grouse collected after the outbreak show that none had antibodies, suggesting that they lack resistance. The spread of WNv represents a significant new stressor on sage-grouse and probably other at-risk species. While managing habitat might lessen its impact on sage-grouse populations, WNv has left wildlife and public health officials scrambling to address surface water and vector control issues in western North America.