It has been reported that regular aerobic activity causes adaptations in the Autonomic Nervous System, modifying cardiovascular parameters. The sportive performance is associated with the individual cardiovascular conditioning, and the heart rate variability analysis (HRV) is a way to evaluate this status. This paper describes the difference between the HRV indexes of athletes and non-athletes, aiming to assist the professionals in the athletes' cardiovascular conditioning evaluation during its training. A system was developed to analyse the indices and had its implementation described.