Japanese-B virus encephalitis (JE) is considered a uniphasic illness with a variable outcome. Biphasic illness patterns have never been reported previously. From an endemic zone in India we observed six patients of JE (from 62 patients treated in 7 years) who had an early relapse resulting in the biphasic clinical course. Five had poor socio-economic status and three had laboratory evidence of nutritional deficiency. Two patients were adults and the other four were children. Fever, rigors, headaches, body aches, altered consciousness, rigidity and tremors predominated the first phase of illness. During the second phase, behavioural changes, dystonia, pen-oral dyskinesia, drooling, mutism and muscle wasting due to anterior horn cell involvement were the important features. Though the serial antibody titres against the JE virus showed a four-fold rise in the initial or late convalescent phases, there was no increase during the second phase of the illness as compared to the first phase. On MRI, fresh lesions appeared during the second phase at the sites known for their involvement in JE, suggesting recrudescence of the virus. One patient survived with major sequelae, two with minor sequelae and the other three had complete recovery. We conclude that some patients with JE may have an early relapse after partial recovery, giving rise to the biphasic illness pattern. A locally prevalent genetic variant of the virus or host factors may be responsible for the altered clinical course of the disease. Biphasic illness does not necessarily mean a bad prognosis.