We performed serial cranial MRI examinations on an 11-year-old boy with Kearns-Sayre syndrome. Proton density (PD)-, T2-weighted and T2-weighted fluid attenuated inversion recovery (FLAIR) sequences revealed progressive high signal intensity areas in the brainstem, globus pallidus, thalamus, and white matter of the cerebrum and cerebellum bilaterally. The probable gliotic lesions in the brainstem may be part of the neurogenic origin of the external ophthalmoplegia in addition to the primary defect of the extraocularmuscle in KSS.