The sensitivity of carnitine palmitoyl coenzyme A (CoA) transferase I to inhibition of its activity by malonyl-CoA is progressively reduced in mitochondria isolated from ischemic cardiac cells as blood flow decreases to 30% or less of the preocclusion flow. The activity of carnitine palmitoyl-CoA transferase I in mitochondria isolated from nonischemic cardiac cells demonstrates incomplete inhibition, even at high concentrations of malonyl-CoA. Kinetic analyses of these data gave results most consistent with the expression of two overt enzyme activities: one activity that is sensitive to inhibition by malonyl-CoA and one activity that demonstrates little or no sensitivity to such inhibition. The decrease in malonyl-CoA-sensitive activity associated with ischemia results from a 13% decrease in the activity of the sensitive component and a corresponding 13% increase in the activity of the insensitive component. Decreased sensitivity of ischemic carnitine palmitoyl-CoA transferase I to inhibition by malonyl-CoA, together with potential fluctuations in the content of malonyl-CoA in tissue, would increase the synthesis of palmitoylcarnitine during ischemia and facilitate return to the use of fatty acid as a preferred metabolic fuel on reperfusion. This apparent conversion occurs concomitantly with a decrease in the free protein thiol content of the mitochondrial membranes isolated from ischemic cardiac cells. Treatment of the mitochondria from ischemic cardiac cells with dithiothreitol in vitro partially reverses the loss in sensitivity to malonyl-CoA, suggesting the possible role of thiol oxidation in the altered metabolism of ischemic mitochondria. Western blot analysis of these mitochondria using an antibody against carnitine palmitoyltransferase II purified from beef heart demonstrates a 68-kDa protein, which under ischemic conditions apparently is decreased by 2 kDa. These results are more indicative of a modification in protein folding of carnitine palmitoyltransferase than proteolytic changes during ischemia.