The regulation by fibrates and dietary fatty acids of the hepatic gene expression of apolipoproteins (apo) A-I and A-II, the major protein constituents of high-density lipoproteins, as well as of acyl-CoA oxidase, the rate-limiting enzyme of the peroxisomal beta-oxidation pathway, was studied in vivo in the rat and in vitro in primary cultures of rat hepatocytes. In primary hepatocytes, different fibrates decreased apo A-I and increased acyl-CoA oxidase mRNA levels, whereas apo A-II mRNA only decreased in level after treatment with fenofibric acid, but not after bezafibrate, gemfibrozil or Wy-14643 treatment. Treatment with fenofibric acid counteracted the increase in apo A-I mRNA levels observed after dexamethasone or all-trans retinoic acid treatment, whereas simultaneous addition of fenofibric acid together with all-trans retinoic acid or dexamethasone resulted in a superinduction of acyl-CoA oxidase mRNA. Addition of the n-3 polyunsaturated fatty acids (PUFAs), docosanohexaenoic acid and eicosanopentaenoic acid, or the fatty acid derivative alpha-bromopalmitate, decreased apo A-I and increased acyl-CoA oxidase mRNA in a dose-dependent and time-dependent manner, whereas apo A-II mRNA did not change significantly. Nuclear run-on experiments demonstrated that fenofibric acid and alpha-bromopalmitate decreased apo A-I and increased acyl-CoA oxidase gene expression at the transcriptional level. When rats were fed isocaloric diets enriched in saturated fat (hydrogenated coconut oil), n-6 PUFAs (safflower oil) or n-3 PUFAs (fish oil), a significant decrease in liver apo A-I and apo A-II mRNA levels was only observed after fish oil feeding. Compared to feeding low fat, liver acyl-CoA oxidase mRNA increased after fat feeding, but this effect was most pronounced (twofold) in rats fed fish oil. Results from these studies indicate that fish oil feeding reduces rat liver apo A-I and apo A-II gene expression, similar to results obtained after feeding fenofibrate. Fibrates and n-3 fatty acids (and the fatty acid derivative, alpha-bromopalmitate) down-regulate apo A-I and induce acyl-CoA oxidase gene expression through a direct transcriptional action on the hepatocyte. In contrast, only fenofibric acid, but not the other fibrates or fatty acids tested, decrease apo A-II gene expression in vitro.