Introduction. Ixodid ticks simultaneously are hosts and vectors of tick-borne encephalitis virus (TBEV), presenting a high risk to humans. Monitoring of the vectors part of TBEV population is usually held by means of express analysis methods (ELISA and PCR), but only isolation and identification of infectious virus is reliable evidence of TBEV circulation in the natural foci. Objectives — to demonstrate the TBEV infection rates of Ixodid ticks from natural TBE foci of Baikal Region, based on comprehensive study, including ELISA, PCR and isolation of virus on laboratory mice (LM) model. Methods. Questing adult Ixodid ticks (n = 20 111, mainly — Ixodes persulcatus Schulze, 1930), were collected in TBE natural foci of Baikal Region during 2013–2020. The suspension on saline solution was prepared from the each tick and analyzed by ELISA first. The samples with positive ELISA results were verified in PCR-RT. Furthermore, randomly selected samples with negative ELISA results were analyzed by PCR. Suspensions with positive ELISA and PCR results have been inoculated to suckling LM intracerebrally. Results. The samples with positive PCR results have been divided into two groups: group 1 — all suspensions with positive ELISA results, group 2 — randomly selected samples with negative ELISA results. The positive PCR results in group 1 made up 70.5 % with average Ct rate 24.9. The positive PCR results in group 2 have been obtained in 2.2 % of cases with average Ct rate 30.7. The isolation on LM model was more successful in group 1 (25.8 vs 13.0 %; р < 0.01; df = 69). Conclusion. ELISA is more useful for study of large amounts of ticks during monitoring of natural TBE foci, offering insight into the epidemically important vectors rate. To get the more full assessment of the ticks’ infection rate one must use ELISA and PCR simultaneously, and sum the results into general rate. For high strains isolation results the LM should be inoculated with the suspensions, which had shown positive both ELISA and PCR results.