Acute encephalitis is a common CNS infectious disease in children. However, there are limited studies concerning about the correlation between the clinical evaluations and neurological outcome. To investigate the value of neurological evaluations, and the correlation between these evaluations and neurological outcomes of acute encephalitis, in the present study we retrospectively evaluated the neurological outcome of 0- to 16-year-old children with encephalitis or meningoencephalitis between 1999 and 2000. Of 101 children enrolled, 4 died and 25 had other neurological sequelae, including epilepsy, headache, developmental delay, and emotional or behavioral changes during the 5 years of follow-up. The causative organisms in patients with neurological sequelae were herpes virus (HSV) 2/2 (100%), influenza 2/3 (67%), mycoplasma 5/12 (42%), and enterovirus 71 2/7 (29%). The important predictors for adverse outcomes were focal neurological signs, multiple seizures or status epilepticus on admission, leukopenia, focal slow waves or continuous generalized delta waves in electroencephalography (EEG), and focal cortical parenchymal hyperintensity in the magnetic resonance imaging (MRI) (p<0.05). Patients with initial presentations of focal neurological signs, papilledema, myoclonic jerks, and status epilepticus tended to have higher incidence of abnormal findings in brain MRI, although not achieving statistic significances. In addition, children with focal spikes or continuous generalized delta waves in EEG also had higher incidence of MRI abnormalities. We conclude that brain MRI studies may be indicated in patients with focal neurological signs, intractable seizure, and focal spikes, focal delta waves, or continuous generalized delta waves in EEG. For those with MRI examinations, focal cortical hyperintensity suggests poorer neurological outcomes.