Abstract Objective. To examine the independent association of total and central body fat and cardiorespiratory fitness with markers of insulin resistance after controlling for several potential confounders in European adolescents participating in the HELENA-CSS (Healthy Lifestyle in Europe by Nutrition in Adolescence Cross-Sectional) study. Methods. We conducted a cross sectional study (the HELENA-CSS) which comprised 1053 (12.5–17.5 years) adolescents from 10 European cities. Weight, height, waist circumference and skinfold thickness were measured, and body mass index (BMI) was calculated. Cardiorespiratory fitness was measured by the 20-m shuttle run test. Markers of insulin resistance were fasting insulin and glucose, and homeostasis model assessment (HOMA). Results. HOMA and insulin were positively associated with BMI, skinfolds and waist circumference after controlling for center, age, pubertal status and cardiorespiratory fitness (all P ≤ 0.01). HOMA and insulin were negatively associated with cardiorespiratory fitness in adolescents with moderate to high levels of total and central body fat (all P ≤ 0.01). Conclusions. HOMA and insulin were associated with total and central body fat in European adolescents. Moreover, cardiorespiratory fitness explained a part of the HOMA and insulin variance in those adolescents with moderate to high levels of total and central body fat, and also, to some extent, in those with low to middle fat mass.