Wheat plants with Aegilops columnaris cytoplasm are characterized by growth inhibition and partial male sterility and show an impaired mitochondrial cytochrome c oxidase activity. We designed this study to clarify the functional relationship between this impaired cytochrome c oxidase activity and possible structural alterations to the mitochondrial genes cox1, cox2 and cox3 that encode three subunits of the cytochrome c oxidase. Using restriction mapping and DNA sequencing, we found major rearrangements in the flanking regions of the cox1 and cox3 genes. In Northern-blot analysis, we detected two different cox3 transcripts and a reduced level of a cox2 transcript, whereas we could not detect a transcript of cox1. These results suggest that rearrangements of the flanking regions of the cox1 gene may result in the severe suppression of its transcription, and subsequently, may lead to the impaired cytochrome c oxidase activity.