PURPOSE: Metabolic syndrome (MetSyn) increases the risk for morbidity and mortality from cardiovascular disease and exercise training is a fundamental factor in the treatment and prevention the clinical components of MetSyn. We conducted this study to investigate how an exercise program affects the risk components of MetSyn and exercise capacity in physically inactive adults. METHODS: Twenty inactive adults were randomly allocated to receive either moderate intensity training (MCT group) or high intensity interval training (HIT group). The MCT group performed aerobic training at an intensity of 55-75% of the walking on a treadmill at 60-80% heart rate max (HRmax) until expenditure of 300 kcal until the end of training. The HIT group performed running on a treadmill during 4 minutes at 85-95% peak HRmax and had a recovery of 4 minutes at 65% peak HRmax until expenditure of 300 kcal until the end of training. A MetSyn z-score was calculated for each subject from triglycerides, HDL-c, fasting glucose, waist circumference, and arterial blood pressure (MAP). Blood lipids and glucose, waist circumference, MAP and exercise capacity were measured at baseline and 12-weeks thereafter. RESULTS: Z-score MetSyn changes were 1.546 (1.575) in the MCT group, −1.249 (1.629) in the HIT group (difference between groups −2.795 [95% CI, 1.276 to 4.311 (P = 0.001)]. Average cardiometabolic risk factors changed −0.133 in the MCT group (p=0.040) and 0.018 (p=0.294) in the HIT group. There was a significant decrease in glucose fasting from 0 to 12 weeks in MCT group (P=0.039) compared to 12 weeks for the HIT group (P=0.001). Waist circumference was significantly reduced at 12 weeks compared to 0 weeks in HIT (P=0.010). Percentage body fat did not change in the MCT group 0.0 (0.8) and decreased in HIT group −1.1 (difference between groups 1.2 [95% CI, 0.1 to 2.4 P = 0.04]). Muscle mass significantly increased throughout the 12 weeks of training in high intensity with significant differences between groups 0.8 kg [95% CI, 0.3 to 1.3 P = 0.027]. MAP was significantly reduced from 0 weeks at 12 weeks in HIT group (P=0.019). CONCLUSIONS: In inactive adults, this study showed that a 12-week HIT program can improve the clinical risk factor profile for MetSyn.