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The purpose of this study is to investigate the effects of conjugated linoleic acid (CLA) supplementation and endurance exercise on the oxidative/anti-oxidative status in rat liver and skeletal muscles. Sprague-Dawley male rats were randomly divided into HS (high-fat diet sedentary group, n = 8), CS group (CLA supplemented sedentary group, n = 8), and CE group (CLA supplemented exercise group, n = 8). For CLA supplementation, 1.0% CLA was substituted for dietary fat. For endurance exercise, the rats swam for 60 min a day, 5 days a week for 8 weeks. The MDA content, Cu, Zn-SOD and Mn-SOD expression in the soleus muscle (SOM) of the CE group improved significantly compared to the HS (p < 0.01) and CS groups (p < 0.05). Moreover, Mn-SOD expression in both the SOM and extensor digitorum longus muscle (EDL) of the CS were enhanced significantly compared to the HS (p < 0.05). From these results, it was suggested that CLA supplementation under the endurance exercise condition may improve the oxidative status by decreasing the MDA content via potential scavenging of Cu,Zn-SOD, and Mn-SOD protein in red muscle, respectively. Therefore, our study demonstrated long-term endurance exercise with CLA supplementation plays a crucial role for maintenance of antioxidative properties in the skeletal muscle of rat.