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Uncoupling protein 3 (UCP3) is a mitochondrial inner membrane protein, which is hypothesized to shuttle nonmetabolized fatty acids, particularly when excessive fatty acids are present. Purpose: Obese Zucker rats (OZR) have systematically elevated levels of fatty acids, with decreased fatty acid metabolism. We hypothesized that basal UCP3 protein expression levels would be elevated in the skeletal muscles of the OZR compared with the lean Zucker rats (LZR). In addition, because aerobic exercise training has been shown to elevate the ability of skeletal muscle to metabolize lipids, we also hypothesized that aerobic exercise training would decrease skeletal muscle UCP3 protein expression and that this would be more pronounced in the skeletal muscles of the OZR. Methods: OZR and LZR were aerobically trained on a motorized treadmill for 55 min·d[-1], 5 d·wk[-1], for 9 wk. UCP3 and oxidative enzymes were measured in plantaris, gastrocnemius, and soleus muscles. Results: Basal UCP3 protein expression was elevated approximately eightfold in the plantaris muscles and threefold in the gastrocnemius muscles of the OZR compared with the LZR (P < 0.05). However, there was no difference in UCP3 protein expression in the soleus muscles of the OZR compared with the LZR (P = 0.34). Furthermore, aerobic exercise training did not significantly alter UCP3 protein expression in the soleus, plantaris, or gastrocnemius muscles of the LZR; however, UCP3 protein expression levels decreased in trained OZR soleus and gastrocnemius muscles compared with controls. Conclusions: The decrease in UCP3 with aerobic exercise training was most notable in the soleus of the OZR. These data demonstrate that the exercise-induced adaptations of UCP3 protein levels are muscle specific in obese animals compared with lean animals. [ABSTRACT FROM AUTHOR]