The activities of carnitine palmitoyltransferases (CPTs) of mitochondrial outer and inner membranes and of peroxisomes have been studied with carnitine analogues, namely DL-thiolcarnitine, DL-sulphocarnitine and L-aminocarnitine, using palmitoyl-CoA or octanoyl-CoA as co-substrate. With sulphocarnitine, both of the mitochondrial CPTs and the malonyl-CoA-sensitive CPT of peroxisomes showed appreciable activity with palmitoyl-CoA, but relatively lower activity when octanoyl-CoA was the co-substrate. The soluble CPT of peroxisomes did not show any activity with sulphocarnitine in the presence of either acyl-CoA. With thiolcarnitine, all of the CPTs showed more activity with palmitoyl-CoA than with octanoyl-CoA. None of the CPTs showed any activity with aminocarnitine and palmitoyl-CoA, but when the acyl donor was octanoyl-CoA, both of the malonyl-CoA-sensitive CPT enzymes showed considerable activity, unlike the malonyl-CoA-insensitive CPT isoenzymes. Aminocarnitine inhibited palmitoylcarnitine formation by both of the mitochondrial CPTs and by the CPT of gradient-purified peroxisomes, but the purified peroxisomal soluble CPT was not inhibited. These results show that the interaction of CPT enzymes with carnitine analogues, as substrates or inhibitors, is influenced by the chain length of the acyl-CoA substrate, and that the use of the appropriate carnitine analogue and acyl-CoA is likely to be useful for the discrimination of the various CPT activities in CPT deficiency disorders.