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Cerebrospinal fluid lymphocyte subsets in patients with tickborne encephalitis (TBE) and in patients with TBE with concomitant neuroborreliosis (double infection) were analysed by flow cytometry. In the TBE group, higher percentages of CD4+DR+ T cells (p = 0.02) and CD25+ T cells (p = 0.0002) were observed, while in the group with double infection, higher percentages of CD19+ cells (p = 0.007), CD8+DR- T cells (p = 0.04), and CD3+CD71 + T cells (p = 0.0002) were found. It was concluded that several differences in immune cell parameters are present between the two groups of patients. Three variables (CD19+ cells, CD3+CD25+ T cells, CD3+CD71+ T cells) were included in the logistic regression model for calculation of probability for double infection. Flow cytometric characterisation of lymphocyte subsets in CSF can further substantiate the diagnosis of concomitant neuroborreliosis in patients with TBE.