Infection with the tick-borne encephalitis virus (TBEV) can result in various neurological complications. At present, there are little data available on laboratory findings that might help predict the clinical course and prognosis of tick-borne encephalitis (TBE). In the present study 100 patients with TBE were examined in respect to various laboratory parameters potentially characteristic for the disease and indicative for the prognosis in TBE. Pleocytosis, impairment of the blood-CSF barrier and intrathecal synthesis of immunoglobulins (IgM > IgG, IgA) were common findings in most patients. On admission to the hospital, 84% of the patients presented with an intrathecal synthesis of TBEV-specific IgM and/or IgG antibodies in the CSF. At follow-up, intrathecal synthesis of TBEV-specific antibodies was demonstrated in all patients studied within 15 days after the first examination, but changes of CSF parameters did not correlate with the clinical course of disease. In contrast to those with moderate course of disease, patients with severe courses of TBE displayed higher cell counts in the CSF and lower concentrations of neutralizing antibodies in serum, and more frequently revealed an intrathecal synthesis of total IgG. TBE-specific oligoclonal IgG antibodies in the CSF were demonstrated only in three patients with prior, incomplete, vaccination against TBE. The severe course of disease in individual patients with TBE may result from a slow or low production of neutralizing antibodies. In these patients, the more intense damage of the CNS tissue is reflected by higher cell counts in the CSF. At onset of disease the presence of a low concentration of neutralizing antibodies in serum and a high cell count in the CSF might indicate an unfavorable course of TBE.