Japanese encephalitis (JE) is the commonest endemic encephalitis but there are very few studies on the radiological changes and these are based on relatively small number of patients. The present study aims at comparing the CT scan and MRI findings in JE and correlate these with the reported histopathological findings. Forty two patients with JE were subjected to detailed neurological examination. Cranial CT scan was carried out in 38 and MRI scan in 31 patients. Haemagglutination inhibition test was carried out in the acute and convalescent sera. The CT scan and MRI findings have been compared. Both CT scan and MRI were available in 28 patients. In 21 patients, CT scans were abnormal and changes included thalamic hypodensity in 15, midbrain and basal ganglia hypodensity in 1 patient each, cerebral oedema in 4 and cortical atrophy with ventricular dilatation in 2 patients. MRI however was abnormal in all 31 patients including 17 with normal CT scan. Cranial MRI revealed either mixed intensity or hypointense lesion on T(1) and hyperintense or mixed intensity lesion on T(2) in thalami in all except two patients. The MRI lesions were also noted in basal ganglia in 11, midbrain in 18, pons in 8, cerebellum and cerebral cortex in 6 patients each and subcortical white matter in 2 patients. MRI was more sensitive than CT scan in revealing thalamic and extrathalamic abnormalities. Thalamic changes may be helpful in the diagnosis of JE especially in endemic area.