Background: Irisin is a new myokine that has a beneficial effects of exercise on energy metabolism. However, irisin response to different intensities of endurance training is not completely understood. Methods: In the current experimental study, 18 male Wistar rats were fed a high-fat diet and 6 rats were nourished a standard diet for 12 weeks. After 12 weeks, obese rats were randomly divided into 3 groups: highintensity training (34 m/min ~85% VO2max), moderate-intensity training (28 m/min ~70% VO2max) and control. Exercise groups trained 5 days/week for 12 weeks on a rodent treadmill. Serum irisin level and gene expression changes were measured using ELISA and Real Time-PCR method, respectively. Results: In high and moderate-intensity endurance training expression of PGC1-α (P=0.001 and P=0.001), FNDC5 (P=0.013 and P=0.049) and UCP1 (P=0.001 and P=0.001) were significantly more than the control group. Serum irisin level only after high-intensity training was more than the control group (P=0.014). A positive correlation was observed between serum irisin and UCP1 in both of high (P=0.017) and moderate-intensity (P=0.046) training groups. Conclusion: High-intensity endurance training has a positive effect on the level of serum irisin. Also, there is a positive correlation between irisin and UCP1 gene expression in subcutaneous adipose tissue. However, irisin isn’t the only factor affecting on exercise-induced UCP1 gene expression. [ABSTRACT FROM AUTHOR]