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Defects of the mitochondrial respiratory chain give rise to a wide range of clinical disorders ranging from isolated myopathy to multisystem disease. These conditions are now being increasingly recognized, especially among the young, and are significant causes of morbidity and mortality. Our understanding of both respiratory-chain function and the disorders which result from its failure has grown enormously since Luft and colleagues described the first case in 1962 (Luft et al, 1962). However, owing to the complexity of the system we still have a great deal yet to learn. This chapter attempts to provide a general understanding of this unique and vital pathway in energy metabolism. We explore how its dysfunction may produce both local and systemic defects and what is known about the inheritance of these disorders. The last two sections deal exclusively with the methods used for investigation and describe some of the clinical presentations associated with defects of each individual complex.