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This study of 170 children in the Czech Republic examines the clinical course and sequelae for tick-borne encephalitis. Evaluated were demographic and epidemiological data, signs and symptoms at admission, clinical course during hospital stay and laboratory findings. Cerebrospinal fluid was analysed for white blood cells, protein, impairment of blood-cerebrospinal fluid (CSF) barrier and tick-borne encephalitis virus (TBEV)-specific antibodies. Subjective complaints and objective neurological deficits were investigated. Tick bites were reported in 74 % of the children. The illness had a biphasic clinical course in 58 % of cases. The second phase was characterized by headache in 98 %, high fever in 86 % (more than 38.5 °C), vomiting in 64 % and meningeal signs in 92 % of children. Meningitis (77 %) dominated over meningoencephalitis (13 %). Inflammatory changes in CSF were found in 90 % of children. Immunoglobulin M (IgM) antibodies against TBEV in serum were found early in the infection in 99 %. IgM positivity lasted up to 1,126 days. Neurocognitive abnormalities were found in 19 (11 %) of children. Acquired aphasia, lasting tremor of the upper extremities, speech impairment, inversion of sleep and wakefulness, abnormal hyperkinetic movements and vertigo were found to be permanent but not progressing. Severe sequelae persisted in two children (1 %) while in three (2 %) were classified as mild or moderate. Conclusion: Tick-borne encephalitis in children has a benign course with minimal sequelae. Meningitis with biphasic course is the prevalent involvement and the duration of IgM antibodies in serum and index of positivity are not decisive for postencephalitic disorders. [ABSTRACT FROM AUTHOR]