Purpose: The aim of this study was compares the effects of 10 weeks High Intensity Interval training (HIIT) and moderate intensity aerobic training (MIAT) on serum levels of homocysteine and some cardiovascular risk factors in overweight inactive men. Methods: In this semi-experimental study, nineteen overweight men voluntarily participated in this study and were randomly divided to 2 Groups: High Intensity Interval training (HIIT) and moderate intensity aerobic training (MIAT). Subjects performed training programs for 10 weeks, 3 sessions per week. The levels of homocysteine and lipid profile were measured before and after 10 weeks of training programs. For statistical data analysis, independent and paired t tests were used and considered significant at a p≤0.05. Results: The results of this study showed that both High Intensity Interval training and moderate intensity aerobic training caused a significant reduction of homocysteine levels (P≤0.05). After 10 weeks of high -intensity periodic exercise, cholesterol levels (p = 0.001), LDL (p = 0.002) decreased significantly and HDL levels were significantly increased (p = 0.001), In MIAT training group, only a significant reduction in cholesterol was found (P=0.006). Conclusion: According to the results of this study, it seems that both High Intensity Interval training and moderate intensity aerobic training have favorable effects in reducing body weight and some cardiovascular risk factors.