Purpose: To compare the effects of six weeks of high intensity interval training (HIIT) vs continuous moderate intensity training (MIT) for improving body composition, insulin sensitivity (SI), blood pressure, blood lipids, and cardiovascular fitness in a cohort of sedentary overweight or obese young men. We hypothesized that HIIT would result in similar improvements in body composition, cardiovascular fitness, blood lipids, and SI as compared to the MIT group, despite requiring only one hour of activity per week compared to five hours per week for the MIT group. Methods: 28 sedentary overweight or obese men (age, 20 ± 1.5 years, body mass index 29.5 ± 3.3 kg/m2) participated in a six week exercise treatment. Participants were randomly assigned to HIIT or MIT and evaluated at baseline and post-training. DXA was used to assess body composition, graded treadmill exercise test to measure cardiovascular fitness, oral glucose tolerance to measure SI , nuclear magnetic resonance spectroscopy to assess lipoprotein particles, and automatic auscultation to measure blood pressure. Results: A greater improvement in VO2peak was observed in MIT compared to HIIT (11.1% vs 2.83%, P = 0.0185) in the complete-case analysis. No differences were seen in the intention to treat analysis, and no other group differences were observed. Both exercise conditions were associated with temporal improvements in % body fat, total cholesterol, medium VLDL, medium HDL, triglycerides, SI, and VO2peak (P < 0.05). Conclusion: Participation in HIIT or MIT exercise training displayed: 1) improved SI, 2) reduced blood lipids, 3) decreased % body fat, and 4) improved cardiovascular fitness. While both exercise groups led to similar improvements for most cardiometabolic risk factors assessed, MIT led to a greater improvement in overall cardiovascular fitness. Overall, these observations suggest that a relatively short duration of either HIIT or MIT training may improve cardiometabolic risk factors in previously sedentary overweight or obese young men, with no clear advantage between these two specific regimes (Clinical Trial Registry number NCT01935323).