Background: Lower heart rate variability has been proven to be associated with a greater risk for developing hypertension among normotensive men, and hypertension is one of the major risk factor of coronary heart disease. Hormonal factors in premenopausal women may cause variance in heart rate variability and impact lipid profile. Objectives: The study was designed to evaluate the relationship of gender and lipid profile with cardiac parasympathetic reactivity. Materials and Methods: Sixty premenopausal and 60 postmenopausal women along with 60 young and 60 elderly, age and body mass index (BMI) matched men without any apparent illness were selected. Cardiac parasympathetic reactivity during Valsalva maneuver, deep breath test, and 30:15 R–R interval ratios were studied and lipid profile analyzed. Results: Lipid profile showed significant increase in values of total cholesterol, low density lipoprotein (LDL), triglyceride, and significant decrease in high density lipoprotein (HDL) values in younger males when compared with premenopausal females and no difference in these parameters were noticed when comparison was done between elderly males and females. Deep breath test and 30:15 R–R interval ratios showed significant decrease in values in younger males when compared with age matched premenopausal females. Total cholesterol, triglyceride, LDL were negatively correlated with parasympathetic function tests; whereas HDL was positively correlated with parasympathetic function tests. Conclusion: Sex hormone levels may alter the autonomic nervous system response and lipid metabolismand lipids play an important role in modulation of autonomic functions.