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Background and objectives: Elevated blood lipids and physical inactivity are known risk factors of atherosclerosis. The objective of this study was to compare effects of four weeks of high-intensity intermittent training (HIIT) and continuous walking on atherogenic indices of obese middle-aged men. Methods: Study population consisted of 36 male teachers aged 35-50 years, with mean body mass index (BMI) of 30.7 ± 3.5 kg/m2 who were working in the city of Galikesh, northeastern Iran. The subjects were enrolled via purposeful sampling and were randomly divided into two experimental groups and a control group. Before and after the intervention, anthropometric characteristics (height, weight and BMI) and blood pressure of each subject were measured. Fasting blood samples were taken from the left brachial vein 12 hours before the first exercise session and 12 hours after the last exercise session to determine lipid profile. Data were analyzed using SPSS 18 at significance level of 0.05. Results: The four-week walking exercise significantly decreased serum levels of low-density lipoprotein-cholesterol (LDL-C) (P=0.001) and triglyceride (P=0.001). In addition, the HIIT program significantly increased high-density lipoprotein level (HDL-C) (P=0.004) and significantly reduced LDL-C (P=0.049), LDL/HDL (P=0.002), triglyceride (p=0.01), BMI (P=0.027) and blood pressure (P=0.002). In addition, the results of ANOVA and (Scheffe test) showed a significant increase in HDL-C (P=0.042) values and a significant decrease in VLDL-C (P=0.032), LDL/HDL (P=0.041), triglyceride (P=0.024), BMI (P=0.048) and blood pressure (P=0.016) of HIIT group compared to the control group. Conclusion: Our findings indicated that HIIT has beneficial effects on some risk factors of atherosclerosis and cardiovascular disease.