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Background: Active commuting is a good opportunity to accumulate physical activity (PA) across the lifespan that potentially might influence central body fat. We aimed to examine the prospective associations of active commuting at 11, 15 and 18 years of age with central body fat at 18 years., Methods: Participants were part of a large birth cohort study in Pelotas, Brazil (n = 3,649 participants). Active commuting, leisure-time PA and income were self-reported at 11, 15 and 18 years. Waist circumference and trunk fat mass were collected at 18 years with the use of a 3-dimensional photonic scanner and dual-energy X-ray absorptiometry, respectively., Results: Active commuting at 11 years was not prospectively associated with central body fat. However, we found that active commuting at 15 and 18 years were prospectively and cross-sectionally associated with central body fat variables, respectively, in boys but not in girls. Also, boys in the highest tertile of accumulated active commuting (i.e., average of active commuting at 11, 13 and 18 years) were associated with -2.09 cm (95%CI: -3.24; -0.94) of waist circumference and -1.11 kg (95%CI: -1.74; -0.48) of trunk fat mass compared to boys in the lowest tertile. Analyses on changes in tertiles of active commuting from 11 and 15 years to 18 years with central body fat variables at 18 years showed that boys who remained consistently in the highest tertile or moved to a higher tertile had lower levels of central body fat compared to those consistently in the lowest tertile., Conclusions: Active commuting throughout adolescence in boys, especially during middle and late adolescence, is associated with lower levels in central fatness before adulthood.