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Introduction: The purpose of this study was to investigate the response of biochemical markers of bone metabolism to aerobic exercise among healthy and sedentary males. Methods: In this quasi-experiment study, twenty two sedentary males (mean age 35.2±3.1 years) were divided into training (n=12) and control (n=10) groups. Subjects of training group did 12 weeks of aerobic exercise. Control group did not participate in any exercise training or physical activity. Serum levels of alkaline phosphatase and Carboxy-terminal telopeptide of type I collagen, vo2max and body fat percent were measured at the beginning and after training. Data were analyzed using independent and paired t-test. Results: No significant difference was observed in the levels of alkaline phosphatase and Carboxy-terminal telopeptide of type I collagen after aerobic exercise; however aerobic exercise resulted in a significant increase in VO2max and a significant decrease in body fat percent in exercise group. Conclusion: The results of this study showed that 12 weeks of aerobic exercise has no effect on biochemical markers of bone metabolism of sedentary males. It seems that the intensity of exercise was not enough to alter bone metabolic markers. [ABSTRACT FROM AUTHOR]