The purpose of this study was to improve the understanding of the relationship between cardiorespiratory fitness (CRF) and the early aetiology of cardiovascular disease. We examined if the levels of traditional and novel cardiovascular disease risk factors were influenced by the levels of CRF in children. A total of 339 randomly selected children aged 9-10 years participated in the Swedish part of the European Youth Heart Study (EYHS). CRF was estimated by a maximal ergometer bike test and dichotomized into low and high categories. Additional measured outcomes included fasting triglycerides, high density lipoprotein cholesterol (HDLc), C-reactive protein, homocysteine, blood pressure, body mass index, sum of five skinfolds and waist circumference. Homeostasis model assessment (HOMA) was computed from insulin and glucose measurements. Body mass index, skinfold thickness, waist circumference and insulin resistance (HOMA) levels were lower both in girls and boys with high CRF compared to those with low CRF. In girls, the levels of Creactive protein were significantly lower in those with high CRF compared with those with low CRF, while HDLc levels showed the opposite pattern. The levels of triglycerides and homocysteine showed a tendency to be lower in girls having low CRF compared to those with high CRF. The results indicate that the levels of several traditional and novel cardiovascular disease risk factors are positively influenced by the levels of CRF in school-aged children. The data call for the development, testing and implementation of preventive strategies with stronger emphasis on CRF, especially for those children with low CRF. They also reinforce the need to include CRF testing in panEuropean Health Monitoring Systems, also among younger individuals.