Background. Levels of overweight have increased and fitness has decreased in children. Potentially, these changes may be a threat to future health. Numerous studies have measured changes in body mass index (BMI), but few have assessed the independent effects of low fitness, overweight and physical inactivity on cardiovascular (CVD) risk factors. Methods. A cross-sectional multi-center study including 1 769 children from Denmark, Estonia and Portugal. The main outcome was clustering of CVD risk factors. Independent variables were waist circumference, skinfolds, physical activity and cardio-respiratory fitness. Results. Both waist circumference and skinfolds were associated with clustered CVD risk. Odds ratios for clustered CVD risk for the upper quartiles compared with the lowest quartile were 9.13 (95% CI: 5.78–14.43) and 11.62 (95% CI: 7.11–18.99) when systolic blood pressure, triglyceride, insulin resistance homeostasis assessment model (HOMA) score, cholesterol: HDL, and fitness were included in the score. When fitness was removed from the clustered risk variable, the association for fatness attenuated and after further adjustment for fitness, only the highest quartiles of the fatness parameters were significant. Fitness showed the same strength of association with the clustered risk score including systolic blood pressure, triglyceride, HOMA score, and cholesterol: HDL with odds ratio for the upper quartile of 4.97 (95% CI: 3.20–7.73). Physical activity was associated with clustered risk even after adjustment for fitness and fatness with an odds ratio for the upper quartile of 1.81 (95% CI: 1.18–2.76). Conclusion. Physical activity, fitness, skinfold and waist circumference were all independently associated with clustered CVD risk.