OBJECTIVE The aim of this study was to analyze lymphocyte subset numbers in cerebrospinal fluid (CSF) from patients with tick-borne encephalitis (TBE) and acute neuroborreliosis. METHODS CSF lymphocyte subsets were enumerated in 42 TBE and nine neuroborreliosis patients using flow cytometry. RESULTS The CSF numbers of CD4+, CD8+, HLA-DR+ and total-T lymphocytes, B lymphocytes, and NK cells were all greater in neuroborreliosis patients than in TBE patients. Neuroborreliosis patients showed positive correlation of CSF protein levels with the numbers of CD4+, HLA-DR+ and total-T lymphocytes. Also, the numbers of CSF B lymphocytes correlated positively with intrathecal Borrelia burgdorferi-specific IgG antibodies. Conversely, TBE patients demonstrated intrathecal protein levels that correlated positively with all investigated CSF lymphocyte subsets. CONCLUSIONS These results suggest an intensive recruitment of lymphocyte subsets into the central nervous system (CNS) during acute neuroborreliosis, whereas TBE is characterized by a lower accumulation of lymphocyte subsets in the CSF.