Obesity-related conditions impose a considerable and growing burden on low- and middle-income countries, including South Africa. We aimed to assess the effect of twice a 10-week multidimensional, school-based physical activity intervention on children's health in Port Elizabeth, South Africa. A cluster-randomised controlled trial was implemented from February 2015 to May 2016 in grade 4 classes in eight disadvantaged primary schools. Interventions consisted of physical education lessons, moving-to-music classes, in-class activity breaks and school infrastructure enhancement to promote physical activity. Primary outcomes included cardiorespiratory fitness, body mass index (BMI) and skinfold thickness. Explanatory variables were socioeconomic status, self-reported physical activity, stunting, anaemia and parasite infections. Complete data were available from 746 children. A significantly lower increase in the mean BMI z-score (estimate of difference in mean change -0.17; 95% confidence interval (CI) -0.24 to -0.09; p < 0.001) and reduced increase in the mean skinfold thickness (difference in mean change -1.06; 95% CI -1.83 to -0.29; p = 0.007) was observed in intervention schools. No significant group difference occurred in the mean change of cardiorespiratory fitness (p > 0.05). These findings show that a multidimensional, school-based physical activity intervention can reduce the increase in specific cardiovascular risk factors. However, a longer and more intensive intervention might be necessary to improve cardiorespiratory fitness.

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