We have studied the alpha-oxidation of phytanic acid in rat liver and human skin fibroblasts in order to try to resolve the controversial issue of the subcellular site of alpha-oxidation of phytanic acid. The results show that isolated mitochondria are able to alpha-oxidize phytanic acid whereas isolated peroxisomes show no phytanic acid alpha-oxidation activity. Intact hepatocytes were found to alpha-oxidize phytanic acid at a rate which is more than 20-fold higher than the activity found in postnuclear supernatant fractions incubated under optimal conditions. The alpha-oxidation of phytanic acid was found to be sensitive to inhibitors of the respiratory chain and an uncoupler of oxidative phosphorylation. Furthermore, the alpha-oxidation of phytanic acid was found to be deficient in cultured human skin fibroblasts with an inherited deficiency of cytochrome c oxidase and in fibroblasts with a deficiency of functional peroxisomes. We conclude that mitochondria are indispensable for phytanic acid alpha-oxidation. Furthermore, we propose that one (or more) of the partial reactions in phytanic acid alpha-oxidation proceeds in peroxisomes leading to the concept that phytanic acid oxidation in the intact cell requires the participation of both mitochondria and peroxisomes.