Abstract: Background and Objectives: Prevalence of overweight and obesity and its associated cardio-metabolic disease risk has become a major public health concern world-wide. This study examined the relationship between physical activity and risk factors of cardio-metabolic diseases among South African children. Materials and Methods: A total of 1361 (boys: n = 678; girls: n = 683) aged 9-13 years South African primary school children participated in the study. Body weight, body height, waist and hip circumferences and blood pressure were measured using standard protocol. Body mass index (BMI) and waist-to-hip ratio were calculated and used in the evaluation of health risks associated with cardio-metabolic diseases. A short version of the International Physical Activity Questionnaire was used to evaluate physical activity levels among the children. Data were coded and analyzed using SPSS software. Results: A total of 67.1 and 32.9% of boys and girls, participated in the study, respectively. A significant low physical activity level of participation was observed in the studied group. Derived physical activity categories as stratified by gender, indicated that 28.8, 56.7 and 14.5% of boys had low, moderate and vigorous mets, respectively. For girls, 26, 59 and 15% low, moderate and vigorous mets, was observed. Conclusion: The South African children had low levels of physical activity which were significantly associated with increased BMI, systolic and diastolic blood pressures.