Objective The effect of regular exercise alone for reducing risk factors for type 2 diabetes and ectopic fat in the liver and skeletal muscle is unknown in youth. Further, the effect of different exercise modalities on obesity-related metabolic risk is unclear. We examined the effects of aerobic versus resistance training without calorie restriction on insulin action, intrahepatic triglyceride (IHTG) and skeletal muscle lipid in obese boys. Methods Forty-one obese boys [BMI≥95th percentile (34.7±4.5 kg/m2), age: 12-18 yrs] were randomly assigned to one of three groups for 3 months: aerobic exercise (AE, 180 min/week, n=14), resistance exercise (RE, 180 min/week, n =16) or a non-exercise control group (n=11). IHTG were assessed by proton magnetic resonance spectroscopy and intermuscular fat was measured by computed tomography. Insulin sensitivity (IS) and insulin secretion were evaluated by a 3-hour hyperinsulinemic- euglycemic and a 2-hour hyperglycemic clamp, respectively. Results Body weight did not change (P＞0.05) in the AE (-0.7±1.4 kg) and RE (-0.2±0.7 kg) groups and increased significantly (P＜0.05) in the control group (2.9±0.7 kg). Compared with controls, cardiorespiratory fitness increased (P ＜0.05)(AE: 32% and RE: 25%) and visceral fat (AE: 17% and RE: 14%) and intermuscular fat (AE: 13% and RE: 25%) decreased (P＜0.05) in both exercise groups. Further, compared with controls, significant (P＜0.05) reduction in IHTG (2.9 to 1.8%) and IS (2.9 to 3.7 mg/kg/min per μU/ml) were only observed in the RE group. There were no changes in acute insulin secretion in the exercise groups. Conclusion Regular exercise without calorie restriction, and independent of exercise modality, is associated with significant improvement in cardiorespiratory fitness and reductions in visceral adiposity and intermuscular fat in previously sedentary, obese, high-risk boys. Resistance exercise has beneficial effects on reducing liver fat and insulin resistance.