A clinical case control study to identify prognostic factors present at hospital admission associated with early sequelae and fatal outcome of acute Japanese encephalitis (JE) was carried out in Gusi county, Henan Province, central China from June to September 1991. A total of 70 patients with laboratory-confirmed acute JE were studied, of whom 3 cases died and 33 cases had neurological or psychiatric sequelae at the end of three months follow-up. The results showed that acute JE at younger age, with higher body temperature, high white cell count in CSF, and deep coma present at hospital admission were markers for unfavorable outcomes (sequelae or fatal). A history of the vaccination was not correlated with the early sequelae and fatal outcome of the disease. The paper suggests that early diagnosis and treatment and universal JE vaccination for all susceptible populations are keys for decreasing incidence of sequelae and fatal outcome of acute JE.