Peroxisome proliferator-activated receptor ␣ (PPAR␣) is a member of the steroid/nuclear receptor superfamily and mediates the biological and toxicological effects of peroxisome proliferators. To determine the physiological role of PPAR␣ in fatty acid metabolism, levels of peroxisomal and mitochondrial fatty acid metabolizing enzymes were determined in the PPAR␣ null mouse. Constitutive liver -oxidation of the long chain fatty acid, palmitic acid, was lower in the PPAR␣ null mice as compared with wild type mice, indicating defective mitochondrial fatty acid catabolism. In contrast, constitutive oxidation of the very long chain fatty acid, lignoceric acid, was not different between wild type and PPAR␣ null mice, suggesting that constitutive expression of enzymes involved in peroxisomal -oxidation is independent of PPAR␣. Indeed, the PPAR␣ null mice had normal levels of the peroxisomal acyl-CoA oxidase, bifunctional protein (hydratase ؉ 3-hydroxyacyl-CoA dehydrogenase), and thiolase but lower constitutive expression of the D-type bifunctional protein (hydratase ؉ 3-hydroxyacyl-CoA dehydrogenase). Several mitochondrial fatty acid metabolizing enzymes including very long chain acyl-CoA dehydrogenase, long chain acyl-CoA dehydrogenase, short chain-specific 3-ketoacyl-CoA thiolase, and long chain acylCoA synthetase are also expressed at lower levels in the untreated PPAR␣ null mice, whereas other fatty acid metabolizing enzymes were not different between the untreated null mice and wild type mice. A lower constitutive expression of mRNAs encoding these enzymes was also found, suggesting that the effect was due to altered gene expression. In wild type mice, both peroxisomal and mitochondrial enzymes were induced by the peroxisome proliferator Wy-14,643; induction was not observed in the PPAR␣ null animals. These data indicate that PPAR␣ modulates constitutive expression of genes encoding several mitochondrial fatty acid-catabolizing enzymes in addition to mediating inducible mitochondrial and peroxisomal fatty acid -oxidation, thus establishing a role for the receptor in fatty acid homeostasis.