Malonyl-CoA is a potent inhibitor of carnitine palmitoyltransferase I (CPT-I), the rate-limiting enzyme for fatty acid oxidation in mitochondria from liver of fed rats. Malonyl-CoA has also been demonstrated to inhibit skeletal muscle CPT-I. This study was designed to determine the rate of decline in malonyl-CoA in muscle during the course of a prolonged exercise bout. Adult male rats were anesthetized (pentobarbital sodium, intravenously) at rest or after running for 5, 10, 20, 30, 60, or 120 min on a treadmill (21 m/min, 15% grade). Malonyl-CoA was then quantitated in the soleus (type I fibers) and in the superficial white (type IIB) and deep red (type IIA) regions of the quadriceps. Malonyl-CoA decreased in red quadriceps from 2.8 +/- 0.2 to 1.4 +/- 0.2 pmol/mg after 5 min and to 0.9 +/- 0.1 pmol/mg after 20 min of exercise. The concentration of malonyl-CoA remained at this level for the duration of the exercise bout (120 min). In white quadriceps, resting values of malonyl-CoA were lower than in red quadriceps, and a significant decline was not observed until 30 min of exercise. A significant decrease in the soleus was observed after 20 min of exercise. This decline in muscle malonyl-CoA may be an important signal for allowing increased fatty acid oxidation during long-term exercise.