Stunting, or linear growth retardation, has been documented in up to half of all children in rural indigenous populations of South America. Stunting is well understood as a signal of adverse conditions during growth, and has been associated with developmentally induced modifications to body composition, including body fat and muscularity, that stem from early growth restriction. This article examines the relation between short stature and three anthropometric indicators of body composition during childhood and adolescence among a rural, indigenous population of forager-horticulturalists. Anthropometric data were collected annually from 483 Tsimane' youth, ages 2–10 years, in 13 communities in the Beni region of Bolivia for 6 consecutive years (2002–2007). Baseline height-for-age was used to indicate stunting (HAZ < −2.0) and compared with z-scores of body mass index (BMI), sum of two skinfolds, and arm muscle area. Multilevel regression models indicate baseline stunting is associated with lower BMI z-scores (B = −0.386; P < 0.001), body fatness (ZSkinfold, B = −0.164; P < 0.001), and arm muscularity (AMAZ, B = −0.580; P < 0.001) in youth across a period of 6 years. When split by sex, there was a stronger relation between baseline stunting and lower skinfold body fat scores among girls (B = −0.244; P < 0.001) than boys (B = −0.080; P = 0.087). In contrast, baseline stunting was associated with lower arm muscularity in both girls (B = −0.498; P < 0.001) and boys (B = −0.646; P < 0.001). The relation between linear growth restriction and indicators of body composition persist into adolescence, providing additional insight into the influence of adverse conditions during growth. Am J Phys Anthropol 153:92–102, 2014. © 2013 Wiley Periodicals, Inc.