The two branched chain fatty acids pristanic acid (2,6,10,14-tetramethylpentadecanoic acid) and phytanic acid (3,7,11,15-tetramethylhexadecanoic acid) were converted to coenzyme A thioesters by rat liver mitochondrial outer membranes. However, these branched chain fatty acids could not be converted to pristanoyl and phytanoyl carnitines, respectively, by mitochondrial outer membranes. As expected, the unbranched long chain fatty acids, stearic acid and palmitic acid, were rapidly converted to stearoyl and palmitoyl carnitines, respectively, by mitochondrial outer membranes. These observations indicate that the branched chain fatty acids could not be transported into mitochondria. The data presented strongly suggest that in rat liver, c~-oxidation of phytanic acid occurs in organelles other than mitochondria.demonstrated that CPTI activity is reversibly inhibited by malonyl-CoA. Recently, it has been shown that malonyl-CoA inhibits peroxisomal, microsomal and plasma membrane carnitine acyl transferases [8,10,13]. Therefore, in order to understand the role of CPTI in fatty acid oxidation, CPTI must be separated from other carnitine acyl transferases. In view of the difficulties in isolating CPTI in the active state, we decided to investigate CPTI activity in highly purified mitochondrial outer membranes from rat liver. We present evidence that branched chain fatty acids with ~-or fl-methyl groups are poor substrates for CPTI, suggesting that these branched chain fatty acids cannot be transported into mitochondria via the carnitine/ acylcarnitine transport system.