Japanese encephalitis is one of the major public health problems in Assam, northeast India. We aimed to elucidated the clinical and epidemiological profile of the disease during several outbreaks in Assam in 3 consecutive years. Cerebro-spinal fluid and or serum samples of 348 out of 773 clinically-suspected viral encephalitis patients admitted to different hospitals during the period June to August of 2000 to 2002 were tested for detection of JE specific IgM antibody, employing MAC ELISA test at RMRC (ICMR), Dibrugarh. Diagnosis was confirmed in 53.7% patients with the ratios of 1.8:1 and 1.4:1 for male to female and pediatric to adult patients respectively. Most of the cases were pediatrics at the age of 7 to 12 years (34.2%). Fever (100%), altered sensorium (81.8%), headache (70.6%), neck rigidity (54.0%), abnormal movement (51.3%), exaggerated reflexes (48.1%), restlessness (44.9%), increased muscle tone (35.3%), convulsion (33.7%) and coma (20.9%) were the major clinical findings. The majority of cases (96.3%) were from rural areas. House surroundings close to water bodies, rice cultivation, association with pigs, and climatic conditions were environmental factors affecting the abundance of the potential mosquito vectors of the disease.