Background: The epidemic of obesity has contributed to the rapid rise in comorbid conditions such as cardiovascular disease, type 2 diabetes mellitus and hypertension. Aim of Study: The aim of this study was to determine the effect of exercise on metabolic disorders and mitochondrial dysfunction associated with obesity. Material and Methods: The study was conducted on 60 male albino rats divided randomly into four equal groups: Group I: Control non-trained group; Group II: Obese nontrained group; Group II: Control trained group and Group IV: Obese trained group. Obesity was induced by hydrating rats with 70% fructose solution for 5 weeks. Following induction of obesity and after 8 consecutive weeks of swimming exercise, citrate synthase enzyme activity was measured by a kinetic spectrophotometric assay. Plasma insulin level was measured by ELISA and insulin resistance was assessed using (HOMA-IR index), while plasma levels of glucose, triglycerides and total cholesterol were determined by colorimetric assay. Results: The levels of glucose, total cholesterol, triglycerides and insulin resistance were significantly increased in obese non-trained group but significantly decreased in obese trained group compared to control groups. Also citrate synthase activity was significantly increased in obese trained group compared to obese non-trained group. Conclusion: Endurance exercise results in improvement of obesity and glucose homeostasis.