The present study proposes to measure and quantify the heart rate variability (HRV) changes during effort and to test the capacity of the produced indices to predict cardiorespiratory fitness measures. Therefore, the beat-to-beat cardiac time interval series of 18 adolescent athletes (15.2 +- 2.0 years) measured during maximal graded effort test were detrended using a dynamical first-order differential equation model. Heart rate variability was then calculated as the standard deviation of the detrended RR intervals within successive windows of one minute. The variation of this measure of HRV during exercise is properly adjusted by an exponential decrease of the heart rate. The amplitude and the decay rate of this exponential trend are strongly associated with maximum oxygen consumption, maximal aerobic power, and ventilatory thresholds. It indicates that among athletes with better fitness, HRV has higher values at low heart rate and decreases faster when the heart rate increases during exercise. This analysis, based only on cardiac measurements, provides a promising tool for the study of cardiac measurements generated by portable devices.