For tick-borne encephalitis (TBE), as for many other viral diseases, vaccination is the best approach to reduce morbidity. Antibody titer is considered as the gold standard for vaccination efficiency evaluation, whereas T-cells response is equally important and informative. Therefore, study of T-cell response to immunization can give a new insight in antiviral defense and inform new vaccine development.For our research we took PBMC from five donors and isolated leukocyte fractions at six timepoints during two-step TBE-vaccination. At several timepoints IFNγ-producer and CD137+T-cell small fractions were collected. RNA was isolated, TCRβ cDNA, RNA-seq and HLA-alleles libraries were prepared and sequenced using Illumina HiSeq.Deep TCR repertoire profiling was performed. By implementing two different mathematical approaches hundreds of significantly expanded T-clones were found . These clonotypes were detected in small fractions. The discovered T-clones had comparable peaks at different timepoints, that allows us to hypothesize about T-cell recruitment at various response stages. Response strength was connected with infection before vaccination. In this case response was moderate, but independently of donor status T-clones were at the same level on the 75th day. This is the additional evidence of successful immunity training despite light infection in two weeks before vaccination. T-clones of donors with the same HLA-allels formed amino acid sequence clusters reflecting similar specificity. That is an important observation in absence of TBE virus tetramers. Also we observed different immune associated genes expressions. These results help deepen the understanding of T-clones behavior during immunization.