Objective To analyze the relationship of electroencephalographic (EEG) in Japanese encephalitis (JE) with CT, MRI and prognosis and to explore the clinical value of EEG in diagnosing JE. Methods Sixty two patients with JE were examined by EEG, CT and MRI. Follow-up examination was undertaken at 1 and 3 months after hospitalization. Results The abnormal incidence of EEG in 62 JE patients was 100% and higher than that of MRI (χ²=5.37,P=0.02) and CT (χ²=23.15,P<0.01). Two patterns of EEG were noted which included diffuse continuous delta and epileptiform discharges of spikes or sharp waves. Eight patients died in the acute stage and 10 patients were lost from follow-up. At 3 months, 21 patients had complete, 15 partial and 8 poor recovery. The EEG pattern did not correlate with the outcome (P=0.75). Conclusions In JE, EEG shows diffuse continuous delta and epileptiform discharges of spikes or sharp waves occasionally. Although there is no correlation of EEG pattern with the outcome of JE, the abnormal incidence of EEG is high and EEG can be used as reference for early diagnosis in JE disease.