Introduction: There is lack of data about the effects of aerobic training in hypobaric status on metabolic risk factors. Materials and Methods: Thirty-nine middle-aged sedentary male volunteers with metabolic syndrome (Mets) were randomized into four groups, including the normobaric control (NC), hypobaric control (HC), normobaric exercise training (NT) and hypobaric exercise training (HT) groups. Both aerobic training groups (NT and HT) participated in running exercises on a treadmill (three sessions per week) for six weeks, 30 min per session, at 50% of HR max based on Karvonen's formula. Both the control groups (NC and HC) remained inactive during the six weeks of the study, sitting in the barometric chamber, watching TV or studying. Barometric pressure was adjusted to 3000 meter altitude at hypobaric conditions. Results: In both the NT and HT groups, all the metabolic risk factors (waist circumference, mean atrial pressure, blood sugar, triglycerides, high density lipoprotein and Mets overall z score) and body weight were significantly changed however the rate of waist circumference decrease was sharper in the NT group (P<0.05). Hypobaric exposure (HC) also significantly decreased fasting blood sugar and Mets overall z score (P<0.05). Conclusion: The beneficial effects of inactive exposure to hypobaric conditions on overall metabolic state and blood glucose, indicates its therapeutic properties. However, the effects of hypobaric exercise training were not better than those of normobaric exercise on each metabolic risk factor, findings which confirm that promotion of physical fitness and hypobaric exposure could be instrumental in the control of metabolic risk factors.