Body mass index (BMI) does not allow to discriminate the composition of the different body compartments. This study points to the formulation of reference values of fat mass index (FMI) and fat-free mass index (FFMI) in healthy adolescents by means of anthropometric techniques, and the subsequent availability in clinical practice as reference charts. The following is a cross-sectional study in a group of 1040 healthy Caucasian adolescents (470 boys and 570 girls), aged 10.1 to 14.9 years. Weight, height and skinfold thickness were registered, and BMI, percentage of total body fat, FMI and FFMI, and FMI and FFMI percentiles were calculated. Boys show a significant increase in FFMI and a decline in body fat and FMI. By contrast, girls show an increase in body fat, FMI and FFMI. Except for the 10 years, FMI was higher (p < 0.05) in girls in all ages and FFMI was higher (p < 0.05) in boys in all ages. There were no significant differences in the values of BMI between sexes in all ages. The availability of reference values for FMI and FFMI in daily clinical practice would be helpful in the diagnosis and assessment of changes in body composition during the treatment of childhood obesity.