In this TBE cohort, the genotype distribution of TLR3 rs3775291 was 44.4% for homozygous wild type, 41.4% for heterozygous, 14.1% for mutant homozygous genotype, and was in concordance with the distribution among the cohort of Lithuanian TBE-naive controls and among the AME cohort, and did not differ when compared with the combined control cohort (p = 0.135). This evidence concerns the gene TLR3 and tick-borne encephalitis.