SummaryDefects in a pathway as complex as the electron transport chain cause a variety of clinical abnormalities, which vary from fatal lactic acidosis in infancy to mild muscle disease in adults. The primary defect may reside in the nucleus or the mitochondrial genome. Until relatively recently, biochemical assays were the definitive means of establishing a defect of the electron transport chain. However, identification of mtDNA abnormalities allows defects to be defined more precisely and in a number of cases provides an easier (more reliable) means of investigation. Despite advances in this field, disorders of the electron transport chain still remain underdiagnosed. This review attempts to provide a general outline of the biochemistry and molecular genetics associated with these disorders and some of the factors involved in establishing a diagnosis in those patients with a suspected defect of the electron transport chain.