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[Purpose] The aim was to investigate the effects of university students’ smoking and aerobic exercise on metabolic syndrome risk factors. [Subjects and Methods] Twenty-three male students were randomly assigned to the following groups: exercise smoker (n=6), non-exercise smoker (n=6), exercise non-smoker (n=6), and non-exercise non-smoker (n=5). A basketball exercise program was conducted three times per week (70 minutes per session) for 8 weeks with exercise intensity set at 50–80% of heart rate reserve. After 8 weeks, the variables of risk factors for metabolic syndrome were obtained. [Results] Systolic blood pressure and diastolic blood pressure were significantly decreased in the exercise non-smoker group and significantly increased in the non-exercise smoker group. Waist circumference was significantly reduced in both exercise groups regardless of smoking and significantly increased in the non-exercise smoker group. Triglyceride, high-density lipoprotein-cholesterol, and fasting plasma glucose showed no differences between the groups. [Conclusion] Obesity and smoking management should be conducted together for students as well as for those with metabolic syndrome risk factors. It is recommended that more students participate in such programs, and exercise programs should be further developed and diversified to prevent metabolic syndrome and cardiovascular diseases.