There are no published data on the economic burden for specific West Nile virus (WNV) clinical syndromes (i.e., fever, meningitis, encephalitis, and acute flaccid paralysis [AFP]). We estimated initial hospital and lost-productivity costs from 80 patients hospitalized with WNV disease in Colorado during 2003; 38 of these patients were followed for 5 years to determine long-term medical and lost-productivity costs. Initial costs were highest for patients with AFP (median $25,117; range $5,385-$283,381) and encephalitis (median $20,105; range $3,965-$324,167). Long-term costs were highest for patients with AFP (median $22,628; range $624-$439,945) and meningitis (median $10,556; range $0-$260,748). Extrapolating from this small cohort to national surveillance data, we estimated the total cumulative costs of reported WNV hospitalized cases from 1999 through 2012 to be $778 million (95% confidence interval $673 million-$1.01 billion). These estimates can be used in assessing the cost-effectiveness of interventions to prevent WNV disease.