Background. Cardiovascular (CVD) risk factors have been shown to cluster in some children. This has been shown in children from the age of nine years, but recently we found no clustering in six-year old children. It is uncertain when clustering develops and which parameters are related to the development of clustered CVD risk. Methods. A longitudinal study including 484 children aged six years. Three years later, 434 children participated in a follow-up. The main outcome was clustering of five CVD risk factors: homeostasis assessment insulin resistance (HOMA), total cholesterol: HDL ratio, triglyceride (TG), systolic blood pressure and sum of four skinfolds. Independent variables were physical activity and cardiorespiratory fitness. Results. CVD risk factors were independently distributed in the six-year-olds, and there was no association between composite risk factor score and physical fitness or activity even if there were obese and unfit children in the population. Clustering of CVD risk factors was found at the age of nine years, and the observed number with three or more CVD risk factors was 3.33 (95% CI: 1.41–7.87) times higher than expected if risk factors had been independently distributed. At the age of nine years, the lowest quartile of fitness had 34.9 (95% CI: 8.0–152.5) times higher risk of having clustered risk than the most fit quartile. Conclusion. Clustering of CVD risk factors developed between the age of six and nine years. At nine years of age clustered CVD risk was highly associated with low fitness level.