BACKGROUND: Studies examining the relationship between physical fitness and obesity in children have had mixed results despite their interrelationship making intuitive sense. We examined the relationship between physical fitness and overweight and obesity in a large sample of adolescents in the Republic of Seychelles (Indian Ocean, African region). METHODS: All students of four grades of all secondary schools performed nine physical fitness tests. These tests assessed agility, strength and endurance, and included the multistage shuttle run, a validated measure of maximal oxygen uptake. Weight and height were measured, body mass index (BMI) calculated, and "overweight" and "obesity" were defined based on the criteria of the International Obesity Task Force. We defined "lean" weight as age- and sex-specific BMI <10th percentile. Age- and sex-specific percentiles for each fitness test were calculated. "Good" performance was defined as a result >or=75th percentile. RESULTS: Data were available in 2203 boys and 2143 girls from a total of 4599 eligible students aged 12-15 years. The prevalence of overweight (including obesity) was 11.2% (95% confidence interval: 9.9-12.4) in boys and 17.5% (15.9-19.1) in girls. For 7 of the 9 tests, the relationship between BMI and fitness score, as assessed by locally weighted regression, was characterized by a marked inverse J shape. Students with normal body weight achieved "good" performance markedly more often than overweight or obese students on 7 of the 9 tests of fitness and more often than lean children. For example, good performance for the multistage shuttle run was achieved by 25.6% (SE: 2.1) of lean students, 29.6% (0.8) of normal weight students, 7.9% (1.3) of overweight students and 1.2% (0.9) of obese students. CONCLUSION: This cross-sectional study shows a strong inverse relationship between fitness and excess body weight in adolescents. Improving fitness in adolescents, likely through increasing physical activity, might need special interventions that are responsive to the ability and needs of overweight children.