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OBJECTIVE: To compare the long term effects of yoga based cardiac rehabilitation program with only physiotherapy based program as an add-on to conventional rehabilitation after coronary artery bypass grafting (CABG) on risk factors. METHODS: In this single blind prospective randomized parallel two armed active control study, 1026 patients posted for CABG at Narayana Hrudayalaya Institute of Cardiac Sciences, Bengaluru (India) were screened. Of these, 250 male participants (35-65 years) who satisfied the selection criteria and consented were randomized into two groups. Within and between group comparisons were done at three points of follow up (i.e. 6th week, 6th month, and 12th month) by using Wilcoxon's signed ranks test and Mann Whitney U test respectively. RESULTS: Yoga group had significantly (p = 0.001, Mann Whitney) better improvement in LVEF than control group in those with abnormal baseline EF (/=23) after 12 months. Yoga group showed significant (p = 0.008, Wilcoxon's) reduction in blood glucose at one year in those with high baseline FBS >/=110 mg/dl. There was significantly better improvement in yoga than the control group in HDL (p = 0.003), LDL (p = 0.01) and VLDL (p = 0.03) in those with abnormal baseline values. There was significantly better improvement (p = 0.02, between groups) in positive affect in yoga group. Within Yoga group, there was significant decrease in perceived stress (p = 0.001), anxiety (p = 0.001), depression (p = 0.001), and negative affect (p = 0.03) while in the control group there was reduction (p = 0.003) only in scores on anxiety. CONCLUSION: Addition of yoga based relaxation to conventional post-CABG cardiac rehabilitation helps in better management of risk factors in those with abnormal baseline values and may help in preventing recurrence.