West Nile virus causes febrile illness in humans with a proportion of cases progressing to meningoencephalitis, encephalitis, hepatitis, and death. Isolates of the virus fall into two genetic lineages, with differences in neuroinvasiveness for mice occurring between strains within both lineages. We used DNA microarrays to compare gene expression in mice infected peripherally with seven lineage 1 and 2 strains confirmed to be of either high or low neuroinvasiveness in mice and associated with severe or benign infection in humans and birds. The 4 strains with highest neuroinvasiveness induced increased expression of 47 genes in the brain, 111 genes in the liver, and 70 genes in the spleen, relative to the 3 least neuroinvasive strains. Genes involved in interferon signaling pathways, protein degradation, T-cell recruitment, MHC class I and II antigen presentation, and apoptosis were identified that may have both pathogenic and protective effects, but increased expression of certain acute proteins, central nervous system specific proteins and proteins associated with T-cell hepatitis, implicate mechanisms related to exalted virulence.