1. 1. Two different pools of carnitine acyltransferases are present in the inner mitochondrial membrane. 2. 2. A new method for the selective assay of the “inner” and the “outer” pools of carnitine acyltransferases has been developed. The acyltransferases are assayed by an isotope exchange method in intact mitochondria in the absence and the presence of external CoASH. Any endogenous external CoASH is removed by oxidation with the disulfide tetrathionate which does not penetrate the inner mitochondrial membrane. 3. 3. This method has been used for the study of the acyl group specificity patterns of the two mitochondrial pools of carnitine acyltransferases in rat, mouse and calf liver. 4. 4. In all three species the greatest activity in the “inner” transferase pool was found with medium-chain acylcarnitines (optimal substrate: C 7). 5. 5. In rat and mouse liver mitochondria the “outer” transferase pool had a specificity pattern different from that of the “inner” pool. These mitochondria had little or no activity with short-chain substrates in the “outer” pool. The optimum medium-chain substrates were C 9 or C 10. 6. 6. The specificity pattern of the “outer” transferase pool was verified by extracting the “outer” transferase by digitonin. 7. 7. In calf liver mitochondria the specificity pattern of the “outer” transferase pool resembled closely that of the “inner” pool. 8. 8. Clofibrate feeding caused increased activities only in the “inner” transferase pool of rat liver mitochondria. The short-chain activity increased 13 times, whereas the medium- and long-chain activities increased only moderately.