Abstract Objective To assess the occurrence of an aggregate risk to cardiometabolic and musculoskeletal health of Brazilian adolescents in the period 2008/09 and 2013/14 and to identify whether there are differences in risk between the genders and in these periods. Methods This was a trend epidemiological study with a quantitative approach, consisting of a voluntary sample of adolescents from 16 Brazilian states. Data were extracted from the database of Brazil Sports Project (Projeto Esporte Brasil). Health-related physical fitness was evaluated based on body mass index, cardiorespiratory fitness, flexibility, and abdominal strength/resistance. Descriptive analysis, chi-squared test, and Poisson log regression were used for the statistical treatment. Results In the years 2008/09, 14.6% of Brazilian youngsters showed an aggregate risk to cardiometabolic health and 17.1% an aggregate risk for musculoskeletal indicators, whereas in 2013/14, the values of the risk indicators were, respectively 40.0% and 22.4%. It was observed that, in the years 2013/14, the risk to the cardiometabolic health of boys was 2.51 times greater than in 2008/09, while for girls, a three-fold increase in risk was observed. Concerning musculoskeletal health, girls showed a 2.21 risk of being in the risk zone in 2013/14 when compared with 2008/09. Conclusion The occurrence of an aggregate risk to the cardiometabolic and musculoskeletal health of Brazilian adolescents increased in the 2008/09 and 2013/14 periods. Regarding gender, an increase in the cardiometabolic and musculoskeletal risk between these periods was observed in girls. As for boys, an increase was observed only in cardiometabolic risk.