The primary objectives of this study were to determine the seroprevalence of West Nile virus (WNV) infection of horses in Saskatchewan in 2003 and to identify risk factors for the infection. Blood samples were collected in August and October from 212 horses in 20 herds in 5 geographic zones. After accounting for within-herd clustering, the proportion of horses that had been infected with WNV, as determined by IgG and IgM antibody response, was 55.7% (95% confidence interval, 44.9% to 65.8%). The proportion of antibody-positive horses differed among herds (0% to 100%) and across ecoregions (20% to 76%). Horses in southern ecoregions were more likely to have either IgM antibodies or IgG concentrations suggesting infection than were horses in northern ecoregions. The use of mosquito-control measures was associated with decreased risk. After accounting for ecoregion, there was no difference between recipients of an inactivated WNV vaccine and nonrecipients in the occurrence of antibodies reflecting natural infection.