Background: Studies have shown that simple Heart Rate Variability (HRV) measurement is useful in screening for and diagnosing Cardiac autonomic neuropathy (CAN). Aim: This study was aimed to assess the usefulness of R-R variability during deep breathing as the earliest predictor of CAN and to evaluate the effect of glycemic status and duration of diabetes on HRV. Materials and Methods: After obtaining ethical clearance and written informed consent, 72 Type 2 diabetic patients and 98 normal controls were administered an autonomic symptom questionnaire and subjected to recording of resting HRV and HRV during 1 minute deep and controlled breathing. Statistical analysis was done by appropriate tests using SPSS 20.0. Results: 44.4% of participants in the diabetic group had symptoms of autonomic dysfunction in contrast to 7.1 % of the control group (p < 0.0001). Resting HRV parameters and indicators of R-R variability during deep breathing like E/I ratio and Delta HR were significantly reduced (p < 0.001) in the diabetic group compared to controls. Subgroup analysis within the diabetic group showed significant decrease in E/I ratio and Delta HR in groups with poor glycemic control. Simple linear regression sought between resting heart rate and E/I ratio showed a highly significant inverse relationship (p = 0.0001). Conclusion: Our findings suggested that R-R variability during 1 minute deep breathing and resting heart rate are reliable and early predictors of CAN. Employing these simple tests in newly diagnosed patients and those in the pre-diabetic state could help control the emergence of CAN.