Mitochondrial disease can lead to clinical abnormalities in any organ system. Both inherited and spontaneous disorders are known. The spontaneous forms can occur as a mitochondrial DNA (mtDNA) mutation early in embryogenesis or, later in life, as somatic mutations that accumulate with age. The inherited forms may arise from any of >100 characterized mutations in mtDNA or from >200 nuclear gene defects that affect proteins required for mitochondrial function. Most dividing cells survive and interact normally despite their mitochondrial defects. Thus post-mitotic, terminally differentiated cells are preferentially affected in mitochondrial disease. This review emphasizes cellular metabolic co-operation and the structural and biochemical diversity of mitochondria as the framework for understanding the clinical spectrum of mitochondrial disease. The principles of the mitochondrial clinical assessment scale I (MCAS-I) are presented to assist in the development of diagnostic spectra of mitochondrial disease.