The question as to whether fitness should be assessed in a European health monitoring system, perhaps from the early stages of life onwards, remains to be answered. We aimed to examine the associations between cardiorespiratory fitness and metabolic risk factors in children. A total of 873 healthy children from Sweden and Estonia aged 9-10 years (444 girls and 429 boys) were randomly selected. A maximal ergometer bike test was used to estimate cardiorespiratory fitness. Additional cardiovascular risk factors were assessed. Significant differences among cardiorespiratory fitness quartiles for the sum of five skinfolds, insulin resistance, triglycerides, and total cholesterol (TC) and high-density lipoprotein cholesterol (HDLc) ratio were shown in girls whereas in boys, the sum of five skinfolds and insulin resistance were significantly different. The lowest sum of five skinfolds and insulin resistance was shown in the highest cardiorespiratory fitness quartile in girls and boys, and the lowest values of triglyceride and TC/HDLc values in the highest cardiorespiratory fitness quartile was observed only in girls. Cardiorespiratory fitness was negatively associated with a clustering of metabolic risk factors in girls and boys. The results add supportive evidence to the body of knowledge suggesting that cardiorespiratory fitness in children is an important health marker and thus should be considered to be included in a pan-European health monitoring system.