Introduction: Obesity is linked to cardiovascular diseases, characterized by endothelial dysfunction, the optimal mode of exercise for controlling obesity of high-intensity interval training or moderate-intensity continuous training has is the however not yet been determined. Materials and Methods: A total of 33 inactive and overweight women, aged 40-50 years with body mass index over 27kg/m2 were randomized to high-intensity interval training, moderate-intensity continuous training or controls. The exercise intervention consisted of 12 weeks of training, and 3 supervised sessions per week. The moderate-intensity group trained continuously for 47 min at 60–70% of maximum heart rate,while high-intensity training consisted 4×4min durations at 85–95% of maximum heart rate with 3 min active breaks in between these, consisting of walking or jogging at 50–60% of maximum heart rate. Protocols were isocaloric. Before and after the completion of the exercise program, blood samples of the subjects were tested for evaluation of lipid profiles and endothelial progenitor cells (CD34, CD133, and CD309). Analysis of variance (ANOVA) and T-student test were applied for data analysis by SPSS version 20 (P<0.05). Result: According to our findings, changes of CD133 in both training groups was statistically significant (P=0.006).The CD309 index increased significantly only in the moderate-intensity continuous training group (P=0.002), whereas changes of CD34 were not statistically significant (P=0.094). Conclusion: Twelve weeks of training exercises, especially high-intensity interval training, may improve some of the markers of endothelial progenitor cells in overweight women, indicating that regular and prolonged exercise can probably be a preventative factor in the incidence of cardiovascular disease.