The purpose of the study was to compare the aerobic fitness (VO (2) peak) between obese and non-obese boys at pre-puberty and examine the effect of body composition on VO (2) peak in this cohort with reference to TaqI polymorphism at alpha-fibrinogen gene locus. Seventy-seven Chinese boys with similar lifestyle participated in the study. Among them, 47 were diagnosed as obese. VO (2) peak was measured by a treadmill test and body composition was assessed via a combined anthropometrical and bioelectrical impedance analysis method. The alpha-fibrinogen genetic polymorphism was detected through PCR-based digestion with TaqI restriction enzyme. The results indicated that VO (2) peak was significantly lower in obese boys compared with normal weight counterparts when the data were expressed either in conventional ratio unit (ml (-1) . min (-1) . lean body weight [LBW] (-1)) or in allometric unit (ml (-1) . min (-1) . body weight [BW] (-2/3)). LBW, fat mass (FM), and body fat content (BF %) all were correlated with VO (2) peak, while LBW was the strongest predictor. The relationship between body composition and VO (2) peak seemed quite comparable across different alpha-fibrinogen genotypes. Significant difference was observed between obese and non-obese boys in terms of the proportion of genotypes and frequency of alleles. T1T1 homozygotes had higher risk for obesity. We came to the conclusion that prepubertal obese boys exhibited impaired aerobic fitness compared with their normal weight peers. VO (2) peak is closely related to LBW and independent of FM. This relationship remains constant irrespective of the TaqI alpha-fibrinogen genotypes that may be associated with fatness in boys.