Introduction: The aim of current study was to compare on the effects of regular aerobic training intensities on PGC1-α- dependent myokine serum changes and to evaluate lipid profile changes in sedentary obese men. Materials and Methods: Thirty-nine obese men with BMI > 27 were selected and were divided into three groups; group I carried out exercise training with 50-60% of maximum heart rate (Low intensity), group II with 70-80% of maximum heart rate (High intensity), and group III do not carried out exercise training (control group). All training groups carried out exercise training for 30 continuous sessions (3 sessions/per-week for 30 to 45 min per session). After initial assessments anthropometrical, VO2max and blood sampling), followed by 10 weeks of exercise training, post-intervention assessments were completed 24 hours after the last training session. Results: Findings were clarified that Irisin was significantly increased in the low intensity group (p=0.005), and increased by twenty-seven percent in high intensity group, difference however not statistically significant (p=0.08). Also, HDL-cholesterol significantly increased significantly in both groups (p<0.05), LDL to HDL-cholesterol ratio decreased significantly (p<0.05). In addition, there were significant relationships between some of the lipid and anthropometrical indices with Irisin (p<0.05). Conclusion: Both of the training interventions had a good effect on of Irisin changes and improvement of lipid profiles in obese subjects. Nevertheless, compared to other intensities, the effectiveness of low intensity training in these subjects was better. In addition, it seems that exercise training can ameliorate Irisin resistance.