In this study, we investigated the effect of biological maturation on maximal oxygen uptake ([Vdot]O(2max)) and ventilatory thresholds (VT(1) and VT(2)) in 110 young soccer players separated into pubescent and post-pubescent groups.. Maximal oxygen uptake and [Vdot]O(2) corresponding to VT(1) and VT(2) were expressed as absolute values, ratio standards, theoretical exponents, and experimentally observed exponents. Absolute [Vdot]O(2) (ml · min(-1)) was different between groups for VT(1), VT(2), and [Vdot]O(2max). Ratio standards (ml · kg(-1) · min(-1)) were not significantly different between groups for VT(1), VT(2), and [Vdot]O(2max). Theoretical exponents (ml · kg(-0.67) · min(-1) and ml · kg(-0.75) · min(-1)) were not properly adjusted for the body mass effects on VT(1), VT(2), and [Vdot]O(2max). When the data were correctly adjusted using experimentally observed exponents, VT(1) (ml · kg(-0.94) · min(-1)) and VT(2) (ml · kg(-0.95) · min(-1)) were not different between groups. The experimentally observed exponent for [Vdot]O(2max) (ml · kg(-0.90) · min(-1)) was different between groups (P = 0.048); however, this difference could not be attributed to biological maturation. In conclusion, biological maturation had no effect on VT(1), VT(2) or [Vdot]O(2max) when the effect of body mass was adjusted by experimentally observed exponents. Thus, when evaluating the physiological performance of young soccer players, allometric scaling needs to be taken into account instead of using theoretical approaches.