To study the effect of physical activity on whole body fat (BF), its regional deposition and the influence of body fatness on physical performance in prepubertal children. Cross-sectional study. A total of 114 boys (9.4+/-1.5 y, Tanner I-II), randomly sampled from the population of Gran Canaria (Spain), 63 of them physically active (PA, at least 3 h per week during the previous year) and 51 nonphysically active (non-PA). Body composition (DXA), anthropometric variables (body circumferences and skinfolds) and physical fitness were determined in all subjects. The PA obtained better results in maximal oxygen uptake, isometric leg extension force, vertical jump (muscular power), and 300 m (anaerobic capacity) and 30 m running tests (speed) than the non-PA. A lower percentage of body fat (% BF) (4 U less, P<0.05), whole BF mass (36% less, P<0.05) and regional fat mass (28, 25, and 30% less in the trunk, legs and arms, respectively, all P<0.05) was observed in the PA compared to the non-PA. The waist and hip circumferences correlated more closely with both the fat mass accumulated in the trunk region and the % BF (r=0.81-0.95, P<0.001) than the waist-to-hip ratio (WHR). The WHR correlated with the percentage of the whole fat mass accumulated in the trunk (PFT) (r=0.52-0.53, P<0.001). In both groups, the PFT increased curvilinearly with the % BF, regardless of the level of physical activity. ANCOVA analysis revealed that total and regional fat masses explained less than 40% of the difference in performance between the PA and non-PA group. The mean speed in the 30 m running test (V30), combined with the height and whole body mass, has predictive value for the BF mass (R=0.98, P<0.001). The % BF may be estimated from the body mass index (BMI) and V30 (% BF=8.09+2.44.BMI (kg m(-2))-5.8.V30 (m s(-1)), R=0.94, P<0.001) in prepubertal boys. Regular participation in at least 3 h per week of sports activities and competitions on top of the compulsory physical education program is associated with increased physical fitness, lower whole body and trunkal fat mass in prepubertal boys.