ABSTRACT: Investigations of long-term exercise interventions in humans to reverse obesity is expensive and is hampered by poor compliance and confounders. In this study, we investigated intrahepatic and muscle fat, visceral and subcutaneous fat-pads, plasma metabolic profile and skeletal muscle inflammatory markers in response to 12-weeks aerobic exercise in an obese rodent model. Six week old male Wistar rats (n=20) were randomized to chow-fed control (Control, n=5), sedentary high fat diet (HFD, n=5), chow-fed exercise (Exercise, n=5) and HFD-fed exercise (HFD+Exercise, n=5) groups. The exercise groups were subjected to 12 week of motorized treadmill running at a speed of 18 m/min for 30 min/day. Differences in post-intervention measures were assessed by ANCOVA, adjusted for baseline body-weight and pre-intervention measures, where available. Post-hoc analyses were performed with Bonferroni correction. Plasma metabolic profile was worsened and fat-pads, ectopic fat in muscle and liver and inflammatory markers in skeletal muscle were elevated in sedentary HFD-fed animals relative to chow-fed controls. HFD+Exercise animals had significantly lower leptin (P=0.0004), triglycerides (P=0.007), HOMA-IR (P=0.065) intramyocellular lipids (P=0.003), intrahepatic lipids (P<0.0001), body fat % (P=0.001), subcutaneous adipose tissue (P<0.0001), visceral adipose (P<0.0001) and total fatmass (P<0.0001), relative to sedentary HFD-fed animals, despite only modestly lower body-weight. mRNA expression of inflammatory markers Interleukin 6 (IL6) and Tumor necrosis factor alpha (TNF?) were also reduced with aerobic exercise in skeletal muscle. Our results suggest that 12 week of aerobic exercise training is effective in improving metabolic health, fat depots, ectopic fat and inflammation even against a high fat dietary background.