Mitochondrial disease is frequently a multisystem disorder which often involves the central nervous system. Imaging finding although diverse are characterized by focal lesions with T2 hyperintensity, which may be most evident on FLAIR imaging and often progress to atrophy. Deep brain structures including brainstem and basal ganglia structures are particularly vulnerable though white matter and cortex may also be involved. In this paper we describe in detail the imaging features of the spectrum of mitochondrial diseases and suggest a scoring technique for recording severity and extent of brain involvement. Although there is overlap between the imaging features of disease phenotypes, magnetic resonance imaging may be useful in supporting the clinical diagnosis. There is little correlation between molecular defect and imaging findings with some noticeable exceptions such as the MELAS syndrome.