The prevalence of Japanese encephalitis (JE) is not uncommon in Taiwan. It tends to occur in the summer and early autumn. The definite diagnosis of JE was according to the results of serological examination and clinical presentation. We report the magnetic resonance (MR) imaging findings of two patients with serologically proved JE. The MR imaging demonstrated bilateral thalamic involvement with abnormal high signal intensities on T2-weighted images (T2WI), fluid-attenuated inversion recovery images (FLAIR) and diffusion-weighted images (DWI). The lesions showed no obvious contrast enhancement. Recognition of such typical MR imaging features associated with appropriate clinical setting will aid in early correct diagnosis and render proper treatment.