The effects of dehydroepiandrosterone (DHEA) and clofibrate on mitochondrial and peroxisomal proliferation and carnitine acyltransferases [mitochondrial carnitine palmitoyltransferase (CPT) and peroxisomal carnitine octanoyltransferase (COT)] were measured in lean and obese female Zucker rats. DHEA increased total hepatic mitochondrial protein twofold; clofibrate increased total hepatic peroxisomal protein more than fivefold. Both DHEA and clofibrate administration increased enzyme activities, immunoreactive protein, messenger RNA levels and transcription rates for the carnitine acyltransferases. Transcription rates and messenger RNA concentration for both carnitine acyltransferases correlated with the increases in activity. These data suggest that the hepatic CPT and COT in female Zucker rats are regulated primarily at the transcriptional level by DHEA and clofibrate.