Although recently the incidence of prehypertension has increased considerably, the pathophysiological mechanisms and the effects of gender in its causation have not yet been fully elucidated. Therefore, in this study body mass index (BMI), waist-hip ratio (WHR), basal heart rate (BHR), blood pressure (BP), rate pressure product (RPP), and spectral indices of heart rate variability (HRV) were reordered and analyzed in normotensive and prehypertensive males and females. It was observed that low frequency-high frequency (LF-HF) ratio, the sensitive indicator of sympathovagal imbalance (SVI), is significantly more (P < .001) in male prehypertensives compared with female prehypertensives. Although SVI in prehypertensives was found to be due to both sympathetic activation and vagal inhibition, contribution of vagal withdrawal was prominent in males. The LF-HF ratio was significantly correlated with BMI, WHR, BHR, BP, and RPP, which was more prominent in male prehypertensives and the degree of correlation was more for WHR and diastolic pressure. It was concluded that vagal inhibition plays an important role in critical alteration of SVI in the genesis of prehypertension, especially in males, and WHR could be a better indicator of SVI in prehypertensives. It was suggested that prehypertensives should improve their vagal tone to restore the sympathovagal homeostasis.