The effects of three peroxisome proliferators on the mRNA levels for some mitochondrial inner-membrane proteins in rat liver were investigated. Clofibrate, perfluorooctanoic acid, and acetylsalicylic acid all increased the mRNA levels for the mitochondrial-encoded respiratory-chain components cytochrome c oxidase subunit I and NADH dehydrogenase subunit I. Mitochondrial 16S rRNA was also induced by clofibrate. The mRNA levels for the nuclear-encoded mitochondrial inner-membrane proteins adenine nucleotide translocator and cytochrome c1 were selectively induced by the different peroxisome proliferators. Malic enzyme, which is induced by thyroid hormone, was also induced by the three peroxisome proliferators tested. These effects are in some ways similar to those obtained with thyroid hormone.