Introduction: Accurate and sensitive measurement of body composition is an important tool in the diagnosis and control of obesity. Objective: To compare body fat changes measured by dual-energy X-ray absorptiometry (DXA), bioelectrical impedance analysis (BIA), and skinfolds (SK) in healthy overweight adults in order to evaluate whether all three methods can be used during a weight loss program (WLP). Methods: Eighty-four men (n=36) and women (n=48), body mass index 25–29.9 kg/m2, aged between 18-50 years, non-smokers and sedentary, were randomly assigned to strength, endurance, combined strength plus endurance, or physical activity recommendations groups. All subjects followed a hypocaloric diet (25-30% decrease in energy intake in terms of the total daily energy expenditure). The intervention lasted 22 weeks. Results: The highest correlation was obtained between DXA and SK when men and women were studied together (r=0.864, p<0.01). In women, significant differences were found between DXA and BIA in fat percentage (underestimation of BIA 2.4%, p<0.05). The underestimation was more determinant for both fat percentage and fat mass in men, 13.2% versus 10.2%, and 6.8 kg versus 4.2 kg between BIA and SK respectively (p<0.05). All the procedures obtained similar results (p>0.05) when changes in body fat caused by intervention were analyzed. However, considering results of the minimal difference compared to DXA, BIA showed the greatest sensitivity to detect changes in fat percentage and fat mass, while SK underestimated the changes, with a significantly lower percentage considered real (p=0.01). Conclusion: The SK method seems to underestimate real changes, therefore DXA and BIA can serve as more effective tools to measure the change in fat percentage and fat mass during WLP. Level of evidence II, Diagnosis.