Introduction and background: In sports medicine, heart rate variability (HRV) analysis is used to assess adaptation to athletes' training. Our goal was to validate HRV analysis as a health indicator by comparing HRV parameters with Short Form-12 Health Survey Questionnaire (SF-12) scores in a sample of healthy individuals. Methods: We performed an experimental study in 32 healthy individuals (18 men and 14 women) with a mean age of 26.19 years. The SF-12 questionnaire was used to evaluate quality of life and a S810i Polar heart rate monitor was used to recode HRV through the R-R interval. HRV parameters were obtained with Polar Precision Performance software. Results: The root mean square of the differences between adjacent R-R intervals in milliseconds (RMSSD), the percentage of the adjacent R-R intervals differing by more than 50 milliseconds in the entire recording (pNN50) and the high frequency (HF) parameters of HRV showed a significant and positive correlation with the perceived physical health scores obtained in the physical component summary scale, the role-physical dimension and the total scale of the SF-12 questionnaire. Participants with greater perceived health showed the highest HRV. Higher parasympathetic activation at rest was related to greater health-related quality of life. Conclusions: Our results confirm that HRV analysis is a good marker of health status and could be used to diagnose stress states (overtraining, burnout, fatigue, exhaustion, anxiety) quickly and easily (at rest and non-invasively), both in the general population and, in particular, in elite athletes.