We investigated the effects of hypoxia and intermittent hypoxia in rat muscle by quantitating the expression of genes encoding cytochrome c oxidase (CytOx) subunits I, II and IV, and ribosomal 12S RNA. The quantitative assessment was made by CE in a polymer network, laser being used to facilitate the detection of induced fluorescence. Constant and intermittent hypoxia influence gene expression and ribosomal activity to different degrees. We found constant hypoxia to be accompanied by an increment in the mitochondrial CytOx subunit transcripts II and I and 12S ribosomal subunit, whereas the nuclear subunit (IV) remained unchanged. No changes were observed in intermittent hypoxic rats. Despite the increment in messenger expression, the decrease in enzyme activity was accompanied by a decrease in citrate synthase activity, a marker of mitochondrial function. The increment in CytOx mitochondrial subunits messengers and ribosomal 12S RNA under prolonged chronic hypoxia could be a consequence of reduced protein synthesis that leads to messenger accumulation.