Mitochondrial DNA disorders are an important cause of neurological disease, yet despite our awareness of the importance of these conditions, relatively little is known about the neuropathology of these disorders and even less about the mechanisms involved in neuronal dysfunction and death. In this review we detail important features from neuropathological studies available and highlight deficiencies that are currently limiting our understanding of mitochondrial DNA disease. We also discuss possible future approaches that might resolve some of these outstanding issues. Further study of these disorders is critical because mitochondria play a central role in neuronal survival and it is likely that an understanding of the mechanisms involved in neuronal dysfunction and cell death in mitochondrial DNA disease may have implications for other neurodegenerative diseases.