This comparison of allele distributions across groups of WNV+ subjects with different infection outcomes revealed higher frequencies of the alleles HLA-A*68, HLA-C*08, and HLA-DQB1*05 in subjects experiencing neuroinvasive disease than in asymptomatic subjects, and these alleles were present at intermediate frequencies in symptomatic subjects. Here, HLA-DQB1 is linked to glycogen storage disease VI.