The aim of this study was to assess the association between physical fitness and clustering of cardiovascular disease (CVD) risk factors in boys and girls aged 9 years (children) and 15 years (adolescents). Subjects were 1020 randomly selected children and adolescents. Cardiorespiratory fitness was assessed by a maximal cycle ergometer test. A subject was defined as having a risk factor if he/she belonged to the upper quartile of risk within age and gender group for that risk factor. Clustering was analysed in relation to being at risk in a) three or more and b) four or more of five possible risk factors (TC:HDL ratio, insulin:glucose ratio, triglyceride, systolic BP and sum of four skinfolds. Physical fitness was weakly related to single CVD risk factors except sum of skinfolds where the relationship was strong. Low fitness increased the risk of having three or more CVD risk factors with odds ratios (OR) using the upper quartile of fitness as reference of 1.9 (95% CI: 0.8–4.1), 3.0 (95% CI: 1.4–6.3) and 11.4 (95% CI: 5.7–22.9), respectively. Using the criterion of four or more risk factors, an OR of 24.1 (95% CI 5.7–101.1) was found in the low fit group.