Objective: To examine the associations of low-grade inflammation with objectively measured physical activity, cardiovascular fitness (CVF) and fatness in prepubertal children. Design: Cross-sectional study. Subjects: One hundred and forty-two children (74 boys and 68 girls) aged 9-10 years (pubertal stage I and II) from the Swedish part of the European Youth Heart Study. Measurements: Total physical activity and its intensity levels (moderate, vigorous, moderate + vigorous) were measured by accelerometry. CVF was measured with a maximal ergometer bike test. Body fat was derived from the sum of five skinfold thicknesses. The measured low-grade inflammatory markers include C-reactive protein, fibrinogen, complement factors C3 and C4. Results: C-reactive protein and C3 were negatively associated with CVF (beta = -0.254 and -0.267, respectively, P<0.05) and positively associated with body fat (beta = 0.439 and 0.446, respectively, P<0.001), after controlling for sex, age and pubertal development. C-reactive protein and C3 were not significantly associated with CVF once body fat was in the model. Low-grade inflammation was not associated with physical activity, but physical activity was associated with CVF. Conclusions: The results showed that low-grade inflammatory markers were negatively associated with CVF and positively associated with body fat in prepubertal children. For most of the variables, the influence of fatness was slightly higher than the influence of CVF. The findings suggest that the potential beneficial effects of physical activity on low-grade inflammation may be explained by its association with CVF. Understanding the interplay between physical activity, CVF and fatness may be of importance to reducing cardiovascular disease risk in young people.