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Dual-energy X-ray absorptiometry (DXA) has been considered a reference method for measuring body fat percentage (BF%) in children and adolescents with an excess of adiposity. However, given that the DXA technique is impractical for routine field use, there is a need to investigate other methods that can accurately determine BF%. We studied the accuracy of bioelectrical impedance analysis (BIA) technology, including foot-to-foot and hand-to-foot impedance, and Slaughter skinfold-thickness equations in the measurement of BF%, compared with DXA, in a population of Latin American children and adolescents with an excess of adiposity. A total of 127 children and adolescents (11–17 years of age; 70% girls) from the HEPAFIT (Exercise Training and Hepatic Metabolism in Overweight/Obese Adolescent) study were included in the present work. BF% was measured on the same day using two BIA analysers (Seca^® 206, Allers Hamburg, Germany and Model Tanita^® BC-418^®, TANITA Corporation, Sportlife Tokyo, Japan), skinfold measurements (Slaughter equation), and DXA (Hologic Horizon DXA System^®, Quirugil, Bogotá, Columbia). Agreement between measurements was analysed using t-tests, Bland–Altman plots, and Lin’s concordance correlation coefficient (ρc). There was a significant correlation between DXA and the other BF% measurement methods (r > 0.430). According to paired t-tests, in both sexes, BF% assessed by BIA analysers or Slaughter equations differ from BF% assessed by DXA (p < 0.001). The lower and upper limits of the differences compared with DXA were 6.3–22.9, 2.2–2.8, and −3.2–21.3 (95% CI) in boys and …