Higher death rate has been reported in postmenopausal or perimenopausal women with cardiovascular events than in men. Reduced estrogen production from ovaries has been suggested as one of its factors. Studies with estrogen therapy have shown cardio-protective effects. However, estrogen has proliferative effect on breast and its long-term use may be carcinogenic. One of the alternative therapies, yoga has been found to reduce the levels of testosterone and luteinizing hormone in hirsutism. Therefore, we aimed to study the effect of yoga on female sex hormone level and heart rate variability in perimenopausal women. Consenting twenty perimenopausal women were randomized into yoga (n=10, age 44±2.64 years) and control (n=10, age 46±5.09 years) groups. Subjects suffering from any diseases or on medication were excluded from the study. Yoga group practiced meditation, pranayama (breathing exercise) and few easy asnas (postures) for 30 min/day for a month. Control group did not do any yoga/relaxation or any active relaxation procedures. Short-term heart rate variability was recorded in all subjects at zero and one month. Institutional ethical committee approved the work. Both groups were comparable in term of their age, height, weight, BMI, systolic BP, diastolic BP, heart rate, and respiratory rate. Time domain measures of HRV, which are primarily markers of cardiac parasympathetic activity [SDNN: 23.93(18.5-35.4) vs 43.2(34.4-50.1) ms, p=0.014; rMSSD: 17.3(12.45-21.85) vs 30.6(25.15-38.05) ms, p=0.022; NN50: 1(0.25-8.5) vs 34(11-60.5) count, p=0.022] were found increased in yoga group as compared to control group after yoga. High frequency power, which is also one of the markers of parasympathetic activity, increased in yoga group as compared to control group. Both serum estrogen [11.95(5.05-41.32) vs 24.47(12.54-64.90) pg/ml, p=0.036] and progesterone [0.24(0.10-1.02) vs 2.0(0.25-9.73) ng/ml, p=0.012] levels were found increased in yoga group after yogic intervention. In conclusion, parasympathetic activity, estrogen and progesterone levels increased in perimenopausal women after a month of yoga practice. Increased parasympathetic activity and female sex hormone levels indicate that yoga can be a cardioprotective alternative therapeutic measure in peri-menopausal women.