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Background: Diabetes and hypertension are known to co-exist frequently as adverse cardiovascular risk factors. Both can produce cardiac autonomic neuropathy that can be measured by ECG RR interval-based heart rate variability (HRV). We compared 5 minutes HRV in four groups based on diabetes and hypertension. Methodology: A cross sectional study was done on 203 participants divided into four groups- diabetics, hypertensives, diabetic-hypertensives and normotensive-nondiabetics. They were evaluated for current disease control and five minutes HRV was done in supine condition following standard protocols by Variowin HR Software. HRV parameters of time domain, frequency domain and Poincare plot were compared between groups and associated with gender, glycaemic control and blood pressure control. Statistical significance was set at p 6 years, comparable BMI, poor glycaemic and blood pressure control. As compared to normal groups, three diseased groups exhibit reduced HRV with respect to all three domains of HRV with varying statistical significance. Among diseased groups, HRV was associated with blood pressure control better than glycaemic control but not with gender. LF /HF ratio was the most consistent HRV parameter showing statistical significance in tests. Conclusion: HRV is reduced in both diabetics more than hypertensives; related to blood pressure control more than glycaemic control. It points altered cardiac autonomic balance, and possibility of cardiovascular risk and early detection of it with timely intervention. It also calls for investigation of same for reinforcement of our observations and further exploration.