The purpose of this study was to determine the effects of exercise training on ventricular epicardial fat thickness in obese men and to investigate the relationship between the changes in epicardial fat thickness to the abdominal fat tissue following exercise training. Twenty-four obese middle-aged men (age, 49.4 ± 9.6 years; weight, 87.7 ± 11.2 kg; body mass index (BMI), 30.7 ± 3.3; peak oxygen consumption, 28.4 ± 7.2 mL/kg/min; mean ± SD) participated in this study. Each participant completed a 12-week supervised exercise training program (60-70% of the maximal heart rate; 60 min/d; 3 d/week) and underwent a transthoracic echocardiography. The epicardial fat thickness on the free wall of the right ventricle was measured from both parasternal long- and short-axis views. The visceral adipose tissue (VAT) and subcutaneous adipose tissues were measured by computed tomography. Following exercise training, the epicardial fat thickness was significantly decreased (P < 0.001). The percentage change of epicardial fat thickness was twice as high compared with those of waist, BMI, and body weight of original values (P <0.05). There was a significant relationship (r = 0.525, P = 0.008) between changes in the epicardial fat thickness and visceral adipose tissue with exercise training. Stepwise multiple regression analysis revealed that VAT, SBP, and QUICKI were independently related to epicardial fat thickness (P <0.05). The ventricular epicardial fat thickness is reduced significantly after aerobic exercise training and is associated with a decrease in VAT. These results suggest that aerobic exercise training may be an effective nonpharmacological strategy for decreasing the ventricular epicardial fat thickness and visceral fat area in obese middle-aged men.