Increasing the intensity of physical activity is associated with reduced risk of cardiovascular diseases and this may be the reason why the blood lipoprotein profiles improve. So the aim of this study was to investigate the effect of six weeks of a high intensity interval training (HIIT) on lipid profile of sedentary young men. For this purpose, 18 sedentary young men voluntarily participated in this study and were randomly divided into training group (n=9, age=24.33±1.41 yr, height=176.22±4.91 cm, weight=72.27±6.59 kg) and control group (n=9, age=23.27±2.01 yr, height=180.22±6.88 cm, weight=76.27±7.23 kg). The training group performed the high intensity interval training for 6 weeks and 3 sessions per week. Blood samples were collected before and after six weeks of high intensity interval training in the fasting state. Data were analyzed by paired t test and independent t test. The results showed a significant decrease in body fat percentage of the training group (P=0.019). Although serum concentrations of triglycerides, low-density lipoprotein, total cholesterol and the ratio of total cholesterol to high-density lipoprotein decreased and high-density lipoprotein levels increased, these changes were not statistically significant (P>0.05). These findings indicated that six weeks of HIIT led to an insignificant relative improvement in lipid profile in sedentary young men and a significant decrease in fat percentage of the training group as well. According to these results, implementation of HIIT may be an efficient factor to prevent and improve the cardiovascular disease risk factors in sedentary young men with regard to the time effect.