The aim of our study was to compare the responses of heart rate variability (HRV) with two different types of hormonal substitution therapy (HT) in post-menopausal women (cross-sectional study) and to reveal an effect of HT shortly after beginning of its administration (follow-up study). To elucidate the influence of menopause and effects of different protocols of a HT on autonomic control of heart rate, we evaluated the heart rate variability (HRV) in 5 groups: premenopausal women (n=140), postmenopausal women without HT (n=360), women on HT with conjugated estrogen only (n=168), women on continuous combined estrogen-progesterone HT (n=117), and men (n=140). Frequency-domain of short-term stationary R-R intervals was performed to evaluate the total variance, low frequency power (LF; 0.04-0.15 Hz), high frequency power (HF; 0.15-0.40 Hz), portion of low frequency power (LF%) and ratio of LF to HF (LF/HF). Significantly lower portion of the LF was found in premenopausal women [46.9 (+/-2.7) nu] when compared to untreated postmenopausal women [54.3 (+/-2.9) nu] and men [55.2 (+/-3.0) nu]. Treatment by estrogen only was proved to decrease the LF% [40.1 (+/-2.1) nu] while no effect on HRV was observed in women treated with combination of estrogen and progesterone [57.2 (+/-3.1) nu]. Also the HF was lower in postmenopausal women [4.16 (+/-0.16) ms(2)] than in premenopausal women [4.79 (+/-0.22) ms(2)] and women treated with estrogen only [4.98 (+/-0.25) ms(2)] while in women treated with combined hormonal therapy the average value [3.99 (+/-0.21) ms(2)] did not significantly differ from that of untreated postmenopausal women. The follow-up study also proved increase of high frequency power already after two months of estrogen substitution therapy [4.86 (+/-0.14) ms(2) vs. 4.19 (+/-0.15) ms(2)]. These results suggest that higher vagal modulation of heart rate that seems typical for younger women becomes after menopause similar to that of men. We also proved a positive shift of HRV parameters toward more beneficial values as for a cardiovascular risk in postmenopausal women treated with estrogens but not in those treated by combined estrogen - progesterone substitution therapy.