The aim of the present investigation was to compare the accuracy of the heart-rate (HR) deflection point (HRDP) and the second HR variability threshold (HRVTh2) to predict anaerobic threshold in boys. HRDP was determined from slope trends of successive linear regressions. HRVTh2 was determined from the high frequency's peak and power-density trends. The second ventilatory threshold (VTh2) corresponding to the first decrease in PETCO2, with an increase in VE /VCO2, was used as the reference measure of AnT. Results show that VO2 and HR were similar at HRDP, HRVTh2, and VTh2. HRVTh2 and HRDP were highly correlated. It appears that HRVTh2 is a good alternative to HRDP for assessing anaerobic threshold. HRVTh2 and HRDP might rely on similar mechanisms.