The central nervous system (CNS) is the second most frequently affected organ in mitochondrial disorders (MD). In the majority of the cases, clinical CNS manifestations correlate with the CNS lesions on imaging and vice versa. The most important method to demonstrate CNS abnormalities in MD is the MRI. This imaging technique can demonstrate structural lesions, such as strokelike lesions, focal or diffuse atrophy, cysts or lacunas, focal or diffuse white matter lesions, grey matter lesions of the cortex or deep grey matter, and increased iron deposition. Functional abnormalities such as increased lactate in the white and grey matter or increased cholin in the white matter can be demonstrated by proton spectroscopy. Abnormlities of the intracerebral vessels can also be documented by MRI. Calcification and bleeding, however, are still more easily accessible by CT. Differentiation between disseminated, focal MD lesions of the white matter from nonactive MS plaques requires inclusion of the individual and family history and all instrumental investigations which are usually necessary to establish the diagnosis of a MD.