Acute encephalitis is a relatively uncommon but potentially harmful CNS inflammation usually caused by infection. The diagnosis is difficult to establish and the etiology often remains unclear. Furthermore, the long-term prognosis of acute encephalitis in children is poorly described. In this study, we characterize childhood encephalitis from a Swedish perspective in regard to etiology, clinical presentation and sequele. We retrospectively studied all children (n=93) who were admitted for acute encephalitis at Karolinska University Hospital in Stockholm during 2000-2004. A confirmed etiological agent was identified in eight cases and a probable one in 37; in 48 cases no etiological agent could be found. Tick-borne encephalitis virus, enterovirus, respiratory syncytial virus, varicella zoster virus and influenza virus predominated and represented 67% of all the confirmed or probable etiologies. Encephalopathy was present in 80% of the children, 81% had fever, 44% had focal neurological findings, and seizures occurred in 40%. EEG abnormalities were seen in 90% and abnormal neuroimaging was present in 30%. The cerebrospinal fluid showed pleocytosis in 55%. There was no mortality, but 60% of the children had persisting symptoms at the time of discharge, 41% of which were moderate to severe. We conclude that the etiology of encephalitis among Swedish children is at large the same as in other European countries with similar vaccination programs. Fever and encephalopathy were seen in a majority of children and the most sensitive tool for making the diagnosis was EEG examination. Furthermore, many children display persisting sequele at discharge for which the strongest predictive factor was focal neurological findings at presentation.