The aim of this study was to compare the expression of 12 cytokines, including those associated with innate and early pro-inflammatory immune responses (TNF-α, IL-6), Th1 (IL-2, IFN-γ), Th2 (IL-4, IL-5, IL-13), Th9 (IL-9), Th17 (IL-17A, IL-17F), Th22 (IL-22) cytokines and the anti-inflammatory cytokine IL-10 in different clinical samples (including CSF, serum and urine) of adults with TBE. This evidence concerns the gene IL9 and tick-borne encephalitis.