Objectives: Angina is a symptom of coronary artery disease (CAD). Modulation of cardiac autonomic tone as assessed by heart rate (HR) variability (HRV) is found reduced in patients with CAD; myocardial ischemia, myocardial infarction and some other cardiovascular diseases. Reduced HRV has been found associated with sudden cardiac death in these CAD patients. Several patients present with anginal symptoms clinically in absence of CAD or other diseases. The status of HRV is not much clear in these patients. Thus, we aimed to assess HRV in patients with angina with and without myocardial ischemia and compare it with HRV of healthy subjects of similar age groups and follow-up patients for 1 year for cardiac/health events. Materials and Methods: The study included 61 consecutive male patients clinically presenting with angina and 30 healthy subjects. Based on Thallium-201 myocardial perfusion Single-photon emission computerized tomography (SPECT) imaging, patients were divided into two groups; patients with myocardial perfusion defects (MPD), (n = 33, age 54.91 ± 7.43 years) and patients with no MPD (NMPD), NMPD (n = 28, age 53.04 ± 8.50 years). Short-term HRV was assessed in all patients and subjects in resting supine position following standard protocol. All MPD and 25 NMPD patients could be followed up for 1 year for cardiac/health events. Results: Surprisingly, the NMPD patients showed significantly reduced HRV, Standard deviation of the N-N intervals, The square root of the mean squared differences of successive N-N intervals, Percentage of the number of interval differences of successive N-N intervals greater than >50 ms divided by total number of R-R intervals, low frequency (LF) power, High Frequency (HF) power and total power as compared to both MPD patients and healthy subjects. (Total power [NMPD vs. MPD]: 610.1 [379.9–1072.8] vs. 1508.0 [748.4–2339.4] millisecond squares (ms2), P = 0.001), healthy subjects (Total power: 1414.6 [1104.6-2141.5] ms2, P = 0.001). The markers of sympathetic tone; LF (normalised unit) and LF/HF ratio were higher in NMPD patients as compared to MPD patients resulting in an altered sympathovagal balance. During a 1-year follow-up, sudden death was seen in one MPD patient (3.1%) and two NMPD patients (8%). Conclusion: The NMPD patients showed significantly reduced HRV as compared to both MPD patients and Healthy subjects with an altered sympathovagal balance. Sudden death was also seen in NMPD patients as MPD patients.