The body composition phenotype of low lean mass (LM) has been associated with metabolic disorders and impaired physical functioning in the pediatric population. Abnormalities in body composition may be identified using reference curves; however, no reference data on LM is available for Brazilian adolescents. The purpose of this study was to present reference data, including percentile curves, of whole body LM, lean mass index (LMI), appendicular lean mass (ALM), and fat mass for Southern Brazilian adolescents. This was a cross-sectional study of adolescents aged 12-17 years from a southern region in Brazil, who had body composition assessed using dual energy x-ray absorptiometry (DXA). Percentile values and reference curves employing the Lambda, Mu and Sigma method (LMS) were computed for LM, LMI (lean mass/height2), ALM and fat mass. Data on 541 adolescents (68.6% boys) was included. Sex differences in growth trajectories were observed for absolute and adjusted LM, with boys presenting greater LM quantity with advancing ages than girls (66.9% and 17.4% difference between the ages of 12 and 17 for boys and girls, respectively). The values corresponding to the lowest percentile (3rd) of LMI ranged between 10.63 to 13.93 kg/m2 in boys and 11.13 to 12.03 kg/m2 among girls aged 12-17 years. This study established the first LM, LMI, and ALM reference curves in Southern Brazilian adolescents, which can potentially be used in association with functional measures to identify LM abnormalities during growth.