Relatively little is known about the long-term prognosis for patients with clinical West Nile virus (WNV) infection. We conducted a study to describe the recovery of New York City residents infected during the 1999 WNV encephalitis outbreak. Patients were interviewed by telephone on self-perceived health outcomes 6, 12, and 18 months after WNV illness onset. At 12 months, the prevalence of physical, functional, and cognitive symptoms was significantly higher than that at baseline, including muscle weakness, loss of concentration, confusion, and lightheadedness. Only 37% achieved a full recovery by 1 year. Younger age at infection was the only significant predictor of recovery. Efforts aimed at preventing WNV infection should focus on elderly populations who are at increased risk for neurologic manifestations and more likely to experience long-term sequelae of WNV illness. More studies are needed to document the long-term sequelae of this increasingly common infection.