Introduction: The aim of this study was to determine the effects of cardiac rehabilitation (endurance and resistance exercise training, nutrition and psychological interventions) on metabolic syndrome indexes and exercise capacity in patient with coronery artery disease (CAD).Materials and Methods: We studied 31 patients (21 men and 10 women with mean age of 54.45±7.8 who were participating in the recovery phase II cardiac rehabilitation program and 15 patients (9 men and 6 women with mean age of 55.35±5.7 who were assigned as the control group. Cardiac rehabilitation program (CRP) consists of Exercise program and Dietitian and Psychiatric Counseling. All 46 patients underwent plasma lipids test and Functional capacity was assessed by a maximal exercise test before and after CRP.Results: Both groups were comparable regarding baseline clinical characteristics. Post CRP, functional parameters and plasma lipids criteria improved significantly in the case group as compared to the control.After rehabilitation, the case group demonstrated significant improvements in estimated metabolic equivalents (METs) (8.5+/- 1.8 vs.11.8 +/- 1.5, p<0.001), body weight (73.55+/- 12.84 vs.70.93+/- 12.08 Kg, p< 0.001), body mass index (26.63+/-3.29 vs.25.6+/- 2.93 kg/m2, p<0.01), percent body fat (27.6+/- 9.17 vs.25.88+/- 8.78%, p<0.001), high density lipoprotein (34.08+/- 7.44 vs.52.8 +/- 5.03 mg/dl, p<0.001), low density lipoprotein (131.87+/- 34.9 vs.101 +/- 21.7, p<0.001), a decrease in triglycerides (167.06+/- 54.86 vs.115.71 +/- 25.68 mg/dl, p<0.001), total cholesterol (186.45+/- 43.04 vs.135.45 +/- 23.07, p<0.001) and blood glucose (107.25+/- 26.5 vs.92.06+/-11.09, p<0.0001). There were no changes in any variables for control group.Conclusion: The proposed CRP is effective and might be applied after acute coronary events. The program can be also used as a method of secondary prophylaxis as it lowers total cholesterol, atherogenic index, and body mass index.