Japanese encephalitis (JE) is a leading cause of viral encephalitis in Asia. Mizoram does not have record of JE till now, however, mortality due to ‘viral encephalitis’ among 7 to 20 aged groups during pre-monsoon and post- monsoon season has been recorded. Pathologic studies of fatal human encephalitis caused many common findings. The clinical syndrome may include many neurological effects and many other similarities in the clinical presentations. Such neurologic disease may manifest as subtle changes resulting in an initial misdiagnosis. Several serological methods have been developed for investigation and diagnosis of the disease. However, reverse transcriptase polymerase chain reaction (RT-PCR) based methodologies have resulted in increased sensitivity for the detection of JEV viruses in clinical samples, and offers rapid and sensitive method.