Background: Prolonged pain of musculoskeletal origin can cause changes in autonomic outflow and thereby cardiovascular system. Various studies have been conducted showing the effect of chronic pain on heart rate variability (HRV), but the same study has not been conducted in the population of Eastern Uttar Pradesh. Aims and Objectives: This study was conducted to assess the effects of chronic pain on cardiovascular autonomic control in male cases versus male controls and female cases versus female controls. Materials and Methods: The patients were selected from the pain clinic out patient department with chronicity of >6 months duration and severity of >3 on visual analog scale. Age-sex matched controls were also selected. Electrocardiogram was recorded in the resting state and was analyzed for the HRV by using time and frequency domains. Results: In male cases, maximum RR interval, minimum RR interval, mean RR interval and in female cases, minimum RR is significantly different than male and female controls, respectively (P < 0.05). In frequency domain, low frequency/high frequency (L.F./H.F) ratio in male cases and L.F.m 2 in female cases are different than male and female controls, respectively. Conclusion: The observations reveal that there is a decrease in parasympathetic activity and an increase in the sympathetic activity in the cases as compared to their age-sex matched controls leading to the shifting of sympathovagal balance toward the sympathetic side. The pattern of changes is similar, both in male cases versus male controls and female cases versus female controls with little difference in the magnitude.