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The aim of our study was to investigate the effect of habitual exercise on the autonomic nervous system on the basis of spectral analysis of heart rate variability. We studied 24 healthy subjects. Eight were trained athletes (age 26.9 +/- 12.4 years, weight 58.6 +/- 7.9 kg, BMI 21.7 +/- 2.6 kg/m2) who routinely performed a minimum of 40 minutes of aerobic activity per week. The control population was represented by 16 untrained persons (age 27.1 +/- 11.9 years, weight 59.1 +/- 13.0kg, BMI 22.1 +/- 4.0kg/m2). There was no significant difference in age, gender, weight and BMI between two groups. After 10 minutes of supine resting, all subjects were instructed to perform 40W exercise on a mechanically braked bicycle ergometer for 10 minutes. Heart rate was continuously recorded according to the experimental protocol. Low and high frequency power were calculated by using fast Fourier transform. Differences of parameter values between two groups were examined by using t tests. Before loading, the athletes had a significantly lower heart rate (63.7 +/- 4.0 beats/min) than control subjects (73.0 +/- 9.1 beats/min). During ergometric loading, the coefficient of variation of heart rate (CV) and the high frequency power (HF) were significantly higher, and low frequency power (LF) was significantly lower in the athletes (CV 2.9 +/- 0.6, HF 0.5 +/- 0.2, LF 0.4 +/- 0.2) compared with the control subjects (CV 2.1 +/- 0.8, HF 0.3 +/- 0.1, LF 0.6 +/- 0.1). After loading, the athletes had a significantly lower heart rate. In conclusion, we found that there were significant differences in the spectral components of heart rate variability during exercise between athletes and control subjects. The results show that physical training could possibly increase parasympathetic activity (or decrease sympathetic activity).