To describe the heart rate variability (HRV) of high-level sprinters in both the supine and standing positions, the HRV of 7 male (24±6 yr; 80±8 kg and 182±7 cm) and 11 female (27±5 yr; 61±4 kg; 167±5 cm) high level Brazilian sprinters was measured in the standing and SU body-positions in both the time and frequency domains. The heart rate (HR) and the time (SDNN, RMSSD) and frequency (LF; HF and LF:HF) domains of the HRV were assessed. Natural log-transformations (ln) of all HRV indices were log transformed prior to analysis to reduce bias arising from non-uniformity of error. The Cohen’s effect size and magnitude-based inference (MBI) were obtained for comparisons. The results suggest higher cardiac autonomic stress in the standing position than in the supine for both genders. With the exception of the lnSDNN that showed possibly MBI in female athletes, all other HRV indices presented a likely or almost certainly MBI. Male athletes demonstrated a higher lnSDNN in the SU position (very likely MBI) and a higher HR in the standing position (very likely MBI) than females. In conclusion, elite sprinters (independent of the gender) present lower HRV in the standing position than in the supine position, but males present a more notable change in cardiac autonomic stress than female athletes.