Kearns-Sayre syndrome (KSS) is a rare autosomal dominant mitochondrial disorder affecting the central nervous system. Progressive external ophthalmoplegia is an early and characteristic clinical symptom of the disease. We describe a 22-year-old female patient with a typical KSS including early and severe external ophthalmoplegia. Conventional MRI and diffusion tensor imaging (DTI) was performed to investigate the early involvement of the central nervous system (CNS). DTI revealed substantial white matter alterations that were primarily confined to the brainstem. These early DTI changes support the hypothesis that regional affection of the brainstem may play a role in the pathogenesis of the early oculomotor symptoms. DTI might be helpful to detect an early involvement of the CNS in KSS.