Ageing is associated with a decline in short-term indexes of heart rate variability (HRV). But there is little evidence regarding the extent to which age-related changes in HRV depend on simultaneous changes in levels of estrogen and body composition as it occurs from pre menopausal state to postmenopausal state. The purpose of this study was (i) to compare HRV between pre and postmenopausal women, (ii) to determine whether difference in age, estrogen level and body composition could account for the difference in HRV between these two groups. HRV was assessed using spectral analysis and estrogen level was estimated using radioimmunoassay technique. The body composition, in terms of percent fat, was assessed using measurement of skin fold thickness. Data was analyzed both before and after adjusting for age, estrogen level and body composition. It was found that the total power, high frequency (HF) and the low frequency (LF) power spectrum of HRV in absolute units were significantly lower (P < 0.001) in postmenopausal women compared to that of premenopausal women. Postmenopausal women had significantly lower HF (P < 0.01) and higher LF (P < 0.01) when expressed in normalized units. The ratio of LF/HF, the index of sympathovagal balance was significantly higher (P < 0.01) among postmenopausal women. Analysis after adjusting for age, revealed that age was one of the important confounder, responsible for the differences in all the components of power spectrum between the two study groups. Difference in estrogen level contributed for the difference in relative values of HF and LF components of HRV. Difference in body composition did not explain the difference in HRV between the groups. The study concludes that both ageing and declined estrogen levels are associated with the autonomic alterations seen among postmenopausal women.