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To determine the effects of a 15-week high-intensity intermittent exercise (HIIE) program on subcutaneous and trunk fat and insulin resistance of young women.Subjects were randomly assigned to one of the three groups: HIIE (n = 15), steady-state exercise (SSE; n = 15) or control (CONT; n = 15). HIIE and SSE groups underwent a 15-week exercise intervention.Forty-five women with a mean BMI of 23.2 ± 2.0 kg m−2 and age of 20.2 ± 2.0 years.Both exercise groups demonstrated a significant improvement (P < 0.05) in cardiovascular fitness. However, only the HIIE group had a significant reduction in total body mass (TBM), fat mass (FM), trunk fat and fasting plasma insulin levels. There was significant fat loss (P < 0.05) in legs compared to arms in the HIIE group only. Lean compared to overweight women lost less fat after HIIE. Decreases in leptin concentrations were negatively correlated with increases in VO2peak (r = −0.57, P < 0.05) and positively correlated with decreases in TBM (r = 0.47; P < 0.0001). There was no significant change in adiponectin levels after training.HIIE three times per week for 15 weeks compared to the same frequency of SSE exercise was associated with significant reductions in total body fat, subcutaneous leg and trunk fat, and insulin resistance in young women.