The effects of regular endurance exercise, or acute-exercise and rest on the levels of lipids, carnitines and carnitine palmitoyltransferase-I (CPT-I) were investigated in male Sprague-Dawley rats. The rats were exercise trained on a treadmill for 60 min per day for 60 days (long-term trained, LT), or non-trained for 59 days (NT) and exercised for 60 min on the 60th day. In NT rats, the levels of serum nonesterified carnitine (NEC), acidsoluble acylcarnitine (ASAC), and total carnitine (TONE) increased significantly during the post-exercise recovery period (PERP). In LT rats, ASAC, and TCNE, which increased right after the 60 min running session decreased to the levels of pre-exercise during the PERP. The levels of skeletal muscle ASAC in NT rats, which increased significantly by the acute-exercise, decreased to the pre-exercise levels during the PERP. However, the ASAC level in LT rats reached its peak at 4 h after running for 60 min. Liver triglyceride (TG) and total lipids (TL), which increased by the acute-exercise, decreased to the pre-exercise levels during the PERP in both NT and LT rats. CPT-I activity in NT rats increased significantly after 1 h of a 60-min exercise and slowly decreased to pre-exercise levels during the PERP. However, the CPT-I activity in LT rats, which increased significantly by the 60 min exercise, decreased slowly and reached its pre-exercise level within 8 h of the PERP. Northern blot analysis showed that the changes of CPT-I activities during the PERP coincided with changes in CPT-I mRNA levels. This study shows that both regular endurance exercise, and acute-exercise and rest, can influence differently the levels of carnitines, lipids and CPT-I in rats. The results suggest that regular endurance exercise, rather than the acute-exercise, can change effectively the distributions of carnitines, lipids and CPT-I in rats during exercise and rest.