This study analyzed vegetative modulation, expressed as heart rate variability (HRV) power spectral analysis, in lean and obese women at pre-menopausal or post-menopausal age to reveal possible differences in menopause-related autonomic activity in lean and obese subjects. Sedentary women (n = 40) were divided in four groups: pre-menopausal lean and obese women, post-menopausal lean and obese subjects. The HRV-power spectrum was evaluated on a 5-min long ECG recording. The absolute values of the spectrum were summed in the following frequencies: a low-frequency (0.04-0.15 Hz; LF) and high-frequency (0.15-0.40; HF) range. LF and HF were values used to estimate the sympathetic and parasympathetic activity. LF and HF values of pre-menopausal obese women are lower than values of lean women. The menopause induced a same decrease in LF and HF values in lean and obese subjects, so that no difference was found in post-menopausal groups. This experiment indicates that modifications of autonomic modulation can be included among factors related to obesity in pre-menopausal, but not post-menopausal women.