Introduction: Adiponectin and CTRP-3 as anti-inflammatory and hypoglycemic cytokines play an important role in the metabolic syndrome. The effects of aerobic training on both metabolic risk factors is unknown. Therefore we aimed to investigate the effects of aerobic training on and these cytokines serum adiponectin and Ctrp-3 levels in males with metabolic syndrome.Material and Methods: Twenty five males with metabolic syndrome (age: 56.04±4.37 yrs, weight:98.98±6.62 kg and BMI: 32.52±1.17 kg/m2) were randomized in two groups including the Aerobic Training (n=13) and the Controls (n=12). Aerobic Training subjects were trained for eight weeks at 60-70% of max reserve heart rate, 3 sessions/wk. Blood samples were collected at baseline and 48 hrs following the last training session. Results: Aerobic Training increased serum adiponectin (P=0.002) and plasma HDL levels (P=0.001) and caused decreases in waist circumference(P=0.001), blood glucose (P=0.003) and insulin resistance (P=0.02) ; however, there were no effects on serum CTRP-3 (P=0.30), insulin (P=0.65) and Mean atrial pressure (P=0.12) and plasma triglyceride levels (P=0.24). Conclusion: Serum Adiponectin and CTRP-3 are associated with metabolic risk factors and insulin resistance and aerobic training can improve patients’ metabolic state with synchronized elevation of the circulatory adiponectin level.