Background: Altered autonomic balance has been noted in Irritable bowel syndrome Regular physical exercise may cause restoration of autonomic balance in health and disease. Objective: To assess the effect of brisk walking on the autonomic balance by analysis of heart rate variability in patients with Irritable bowel syndrome (IBS). Methods: This prospective study was conducted in the Department of Physiology, Bangabandhu Sheikh Mujib Medical University (BSMMU) in 2013.Seventy seven male IBS patients aged 20-50 years, were enrolled from Gastroenterology OPD, BSMMU, Dhaka. Twenty eight healthy sedentary male with similar age were control. HRV measures were recorded once prior to exercise and then after 3 months of brisk walking. For assessing autonomic balance, LF/HF ratio and Max/Min RR was evaluated by Polyrite D machine and software. ANOVA, Independent sample t-test and paired t-test were used for statistical analysis. Results: The pre-exercise mean values of LF/HF ratio were significantly higher (p<0.001) in all IBS patients compared to those of control. The post exercise LF/HF ratio were significantly lower (p<0.05) in all IBS patients compared to their pre-exercise values. Conclusion: This study concluded that the sympathovagal balance was towards sympathetic predominance in IBS and regular moderate physical exercise may shift the balance towards parasympathetic predominance in them