Assessing children’s growth adequately is important due to the necessary prevention of adequate body composition, especially at pre-pubertal age. Simpler measurements such as anthropometry or bioimpedance, using equations validated in Caucasian children, have been demonstrated to overestimate or underestimate fat mass percentage (FM%) or fat-free mass (FFM) in Chilean children. In a sample of 424 children (198 boys and 226 girls) of 7–9 years old, the three component (3C) model was assessed, where total body water was determined by 2H dilution and body volume by air displacement plethysmography, in order to design and validate anthropometry and bioimpedance equations. The FM (%) equation specific for Chilean children was validated as (1·743 × BMI z-score) + (0·727 × triceps skinfold) + (0·385 × biceps skinfold) + 15·985, against the 3C model (R2 0·79). The new FFM equation (kg) generated was (log FFM = (0·018 × age) + (0·047 × sex) + (0·006 × weight) + (0·027 × resistance) + 2·071), with an R2 0·93 (female = 1 and male = 2). The Bland–Altman analysis shows a mean difference of 0·27 (sd 3·5) for the FM% in the whole group as well as 0·004 (sd 0·9) kg is the mean difference for the bioelectrical impedance analysis (BIA) FFM (kg) equation. The new equations for FM (%) and FFM (kg) in Chilean children will provide a simple and valid tool for the assessment of body composition in cohort studies or to assess the impact of nutritional programmes or public policies.