Aims/hypothesis Our aim was to examine the association between markers of insulin resistance and: (1) body fat and waist circumference, taking into account cardiorespiratory fitness in school-aged children; and (2) cardiorespiratory fitness at differing levels of body fat and waist circumference. Subjects and methods This was a cross-sectional study of 873 children aged 9.6 +/- 0.4 years from Estonia and Sweden. Weight, height and waist circumference were measured. Body fat was expressed as the sum of five skinfold thicknesses. Cardiorespiratory fitness was estimated by a maximal cycle-ergometer test. The studied markers of insulin resistance were fasting insulin and glucose, and homeostasis model assessment (HOMA). Results HOMA and fasting insulin were positively associated with body fat and waist circumference after adjusting for cardiorespiratory fitness, age, pubertal status and study location. HOMA and fasting insulin were negatively associated with cardiorespiratory fitness in children in the third (highest) tertile of body fat and waist circumference after controlling for sex, age, pubertal status and study location. Fasting glucose was negatively associated with cardiorespiratory fitness in children in the third (highest) tertile of waist circumference, but it was not associated when body fat was taken into account. Conclusions/interpretation In school-aged children, HOMA and fasting insulin are significantly associated with body fat and waist circumference. In addition, cardiorespiratory fitness explains a significant proportion of the HOMA and fasting insulin variance in those children with high levels of body fat and waist circumference. The findings suggest that the deleterious consequences ascribed to high fatness could be counteracted by having high levels of cardiorespiratory fitness.