The aim of the study was to analyze the concentrations of Th1/Th2 cytokines and cortisol in the cerebrospinal fluid (CSF) from patients with aseptic meningoencephalitis (AM). The study enrolled 37 patients with AM and 11 control subjects. CSF concentrations of IL-2, IL-4, IL-5, IL-10, IFN-gamma, and TNF-alpha were analyzed using cytokine bead array and flow cytometry; CSF cortisol concentrations were measured by a RIA method. Cortisol was detected in 37 CSF samples (100%) from patients with AM, and it was significantly elevated in comparison to control subjects. IFN-gamma was detected in 32 CSF samples (86.5%) and IL-10 was detectable in 9 CSF samples (24.3%). The CSF cortisol levels correlated negatively with the duration of AM. The intrathecal concentration of IFN-gamma correlated positively with CSF numbers of leukocytes and lymphocytes, and negatively with the duration of AM. The etiology of AM influenced the CSF cortisol concentration, which was significantly higher in patients with tick-borne encephalitis when compared to persons with AM of unknown origin and control subjects. The results indicate that the prevailing intrathecal immune reaction during AM is shifted to a Th1-like response, whereas anti-inflammatory response in the brain is executed by the effect of cortisol.