alpha-Oxidation of the branched-chain fatty acid, phytanic acid, is defective in patients with Refsum's disease, the disorders of peroxisome biogenesis (e.g., Zellweger syndrome), and in rhizomelic chondrodysplasia punctata. H-3-Release from [2,3-H-3]phytanic acid, which is impaired in cultured skin fibroblasts from these patients, was investigated in rat liver peroxisomes. Cofactors necessary for optimal H-3-release, ATP, Mg2+ and coenzyme A, were also necessary for optimal acyl-CoA synthetase activity, suggesting that the substrate for H-3-release might be phytanoyl-CoA. 5,8,11,14-Eicosatetraynoic acid (ETYA), an inhibitor of long-chain acyl-CoA synthetase activity, blocked phytanoyl-CoA synthesis as well as H-3-release from [2,3-H-3]phytanic acid in a dose-dependent manner. However, this inhibitor had little effect on H-3-release from [2,3-H-3]phytanoyl-CoA. Tetradecylglycidic acid (TDGA) inhibited H-3-release from [2,3-H-3]phytanic acid in peroxisomal but not in mitochondrial fractions from rat liver. This agent inhibited H-3-release from [2,3-H-3]phytanic acid and [2,3-H-3]phytanoyl-CoA equally. In contrast to ETYA, which appeared to decrease H-3-release as a consequence of synthetase inhibition, TDGA appeared to act directly on the enzyme catalyzing H-3-release. This enzyme was partially purified from rat liver. The purified enzyme, which did not possess phytanoyl-CoA synthetase activity, catalyzed tritium release from [2,3-H-3]phytanoyl-CoA. This enzyme catalyzed H-3-release from [2,3-H-3]phytanic acid only if a source of phytanoyl-CoA synthetase was present. We conclude that in rat liver peroxisomes, phytanic acid must be activated to its coenzyme A derivative prior to subsequent alpha-oxidation.