Obesity and hypertension are the major cardiovascular risk factors. Increased QT interval is shown to be associated with various cardiac diseases. The early impact of “prehypertension” on QTc and the contribution of BMI to sympathovagal imbalance are the areas that are least explored. So the objectives of the study were to assess the nature of autonomic dysfunction in prehypertensives by measuring the QTc interval and to evaluate the contribution of BMI to sympathovagal imbalance in the genesis of prehypertension. This was a cross sectional study involving 150 medical students, belonging to age group 18-25. ECG was recorded among all the students and their QTc was measured. Based on their blood pressure recordings and BMI, selected students (n=96) were divided into four groups: normotensives with normal BMI (group 1), normotensives with higher BMI (group 2), prehypertensives with normal BMI (group 3) and prehypertensives with higher BMI (group 4). The level of significance between the groups was tested by one-way ANOVA. The association between QTc and BMI with various blood pressure parameters was assessed by Pearson correlation. The independent contribution of various factors such as age, BMI, BHR, SBP and DBP to sympathovagal imbalance was assessed by multiple regression analysis. QTc was significantly increased among the prehypertensive group compared to the normotensives and the magnitude of these changes were more prominent in subjects with higher BMI compared to that of normal BMI. QTc, an indicator of sympathovagal balance had significant correlation with BMI (P = 0.000) and systolic blood pressure (DBP) (P = 0.002) in prehypertensives. BMI was found to be an independent contributing factor to QTc prolongation (P = 0.0003) in prehypertensives. The significant prolongation of QTc interval among the prehypertensives compared with normotensives indicate the altered autonomic homeostasis and a higher risk of arrhythmias in them, suggesting lifestyle modification at a younger age to reduce the cardiovascular risk.