Using isolated rat liver mitochondria, in the absence or presence of malonyl-CoA (an inhibitor of carnitine palmitoyltransferase I), we have found that carnitine palmitoyltransferase II (CPT II) is active with palmitoyl-CoA as well as with its beta-oxidation intermediates. A partially purified CPT II fraction from rat liver mitochondria was shown to be able to convert 3-hydroxypalmitoyl-CoA to 3-hydroxypalmitoylcarnitine, which could be identified by fast-atom-bombardment mass spectrometry. This apparent broad specificity of CPT II was further evaluated by kinetic studies using purified CPT II. It was found that CPT II readily accepts 3-oxopalmitoyl-CoA, palmitoyl-CoA, 3-hydroxypalmitoyl-CoA and 2,3-unsaturated palmitoyl-CoA as substrates with decreasing order of affinity. The apparent Vmax values found for the first three compounds were of the same order of magnitude; the 2,3-unsaturated acyl-CoA was the poorest substrate. Kinetic studies with purified CPT II showed 3-hydroxypalmitoyl-CoA to have the lowest K0.5 value (20 +/- 6 microM) of all the CoA esters studied; the highest K0.5 value (65 +/- 17 microM) was found for the 3-oxo intermediate. These findings support the hypothesis that CPT II is involved in the export of toxic long-chain acyl-CoA esters from the mitochondria by first converting them into the corresponding carnitine esters, followed by transport out of the mitochondria and subsequently out of the cell.