Tick-borne encephalitis has occurred regularly in Europe since it was first diagnosed in 1931 by Schneider. The mortality rate of patients with this disease is 1-2%. Death usually occurs in the acute stage of illness. A case report of a 28-year-old patient from Slovenia, who died shortly after the onset of tick-borne encephalitis, is described. The clinical course of disease, results of serological tests, neuropathological findings and polymerase chain reaction amplification of parts of viral genome from postmortem brain tissues are presented.