BACKGROUND: Changes in autonomic cardiac function are frequent during menopause, and various methods have been used to understand and minimize them. OBJECTIVE: To study the interference of dynamic aerobic physical activity on heart rate variability (HRV) in climacteric women. METHODS: Cross-sectional study that analyzed HRV in 15 menopausal women (mean age 56.8+/-4.9 years) who had participated in physical training (one-hour walks, 3 times a week) for at least two years (active group), and 15 menopausal women (mean age 56.5 +/- 3.7 years) who were sedentary (sedentary group). None of the volunteers received hormonal replacement therapy. HRV data were compared between the groups by means of the Mann Whitney U Test. RESULTS: There were significant differences both in the frequency and time domains of the following variables of HRV (in medians) for the active e sedentary groups, respectively: total power (22,626.50 ms(2) and 4,432.10 ms(2)), low frequency component (741.20 ms(2) and 131.70 ms(2)), high frequency component (668.90 ms(2) and 131.70 ms(2)), standard deviations of RR intervals (51.60 ms and 22.50 ms), square root of the sum of squares of differences between the normal RR intervals (35.30 ms and 15.90 ms), and percentage of normal adjacent RR intervals greater than 50 ms (6.6% and 0.2%). CONCLUSION: The study suggests that aerobic training may have afforded a significant improvement in the autonomic cardiac function of the menopausal women in the active group, and may be a useful option for preserving this functional condition without the need for hormonal replacement therapy.