Objective: To determine the accuracy of two international Body Mass Index (BMI) cut-offs for classifying obesity compared to the percentage of fat mass (%FM) assessed by Dual-Energy X-ray Absorptiometry (DXA) in a Chilean sample of children and adolescents; Material and Methods: The subjects studied included 280 children and adolescents (125 girls and 155 boys) aged 8 to 17 years. Weight and height were measured. The BMI was calculated. Two international references (IOFT and WHO) were used as cut-off points. The %FM was assessed by DXA. The receiver operating characteristic (ROC) curve was used to assess the performance of BMI in detecting obesity on the basis of %FM; Results: A high correlation was observed between the %FM measured by the DXA and the Z-scores of IOTF and WHO scores in the Chilean adolescents separated by sex (r = 0.78–0.80). Differences occurred in both references (IOFT and WHO) in relation to the criteria (p < 0.001). Both references demonstrated a good ability to predict sensitivity (between 84% and 93%) and specificity (between 83% and 88%) in both sexes of children and adolescents; Conclusions: A high correlation was observed between the Z-score of the BMI with the percentage of fat determined by the DXA. Despite this, the classifications using the different BMI cut-off points showed discrepancies. This suggests that the cut-off points selected to predict obesity in this sample should be viewed with caution.