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The alternative oxidase of the inner mitochondrial membrane catalyses cyanide-insensitive respiration in plants and fungi. The molecular biology and regulation of this oxidase have been intensively studied over the past 10 years. Genes have been isolated, expression has been investigated and novel mechanisms for the regulation of activity have been discovered. This paper reviews these recent advances, focusing on the regulation of gene expression and activation by protein modification and organic acids, and possible roles of the alternative oxidase are discussed.