A prospective study established the etiology of febrile illnesses in residents of Slovenia that occurred within 6 weeks after a tick bite. A combination of laboratory and clinical criteria identified 64 (49.2%) of 130 patients as having confirmed, probable, or possible cases of tickborne disease during 1995 and 1996. Of the 130 patients, 36 (27.7%) had laboratory evidence of tickborne encephalitis, all of whom had clinically confirmed disease. Evidence of infection with Borrelia burgdorferi sensu lato was identified in 26 patients; 10 (7.7%) had confirmed Lyme borreliosis. Of 22 patients with evidence of Ehrlichia phagocytophila infection, 4 (3.1%) had confirmed ehrlichiosis. Infection by multiple organisms was found in 19 (14.6%) of 130 patients. Patients with meningeal involvement (43 [72.3%] of 59) were more likely to have confirmed tickborne disease than were patients with illness of undefined localization (18 [26.5%] of 68; P<.0001). Tickborne viral and bacterial infections are an important cause of febrile illness in Slovenia.