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Patients with viral encephalitis have a high incidence of morbidity and mortality. We analyze the clinical characteristics and outcome of patients with clinically diagnosed viral encephalitis to investigate possible predictors of prognosis. We retrospectively evaluated 1107 patients diagnosed with viral encephalitis in southwest China from 2009 to 2012 by evaluating their outcomes using the Glasgow Outcome Scale. We compared patient outcome at hospital discharge with long-term follow-up visits, and evaluated the prognostic indicators of the outcome. At hospital discharge, 375 (33.9 %) of the 1107 patients who survived made a full recovery, while 399 (36.0 %), 160 (14.5 %), and 145 (13.1 %) had mild, moderate or severe neurologic sequelae, respectively. Twenty-eight (2.5 %) of the patients died prior to discharge from the hospital. Of the 1027 patients who had follow-up assessments, 658 (64.1 %) made a full recovery, while 213 (20.7 %), 103 (10.0 %), and 19 (1.8 %) had mild, moderate or severe neurologic sequelae, respectively. Six (0.6 %) of the patients died after discharge from the hospital. Use of mechanical ventilation, lower Glasgow coma score, and concurrent seizures are predictors for a poor outcome in patients both at hospital discharge and at long-term follow-up visits. [ABSTRACT FROM AUTHOR]