BACKGROUND Metabolic syndrome, physical inactivity and central obesity contribute to early vascular aging, which leads to increased risk of cardiovascular disease. The study aimed to assess the effect of heart rate (HR) targeted aerobic exercise training on the indices of early vascular aging, in particular, arterial stiffness, and on anthropometric and clinical profile of metabolic syndrome subjects. METHODS 126 metabolic syndrome subjects were randomly selected. Anthropometric parameters, blood pressure (BP), blood sample, arterial wall functional and structural parameters were obtained before and after the 8 week (84 pts) supervised training program. The age and gender matched control group (42 patients) followed the same protocol, except for the HR targeted training program. RESULTS In the study group, HR targeted training was associated with decreased aortic pulse wave velocity (8.47 ± 1.40 vs. 8.01 ± 1.06 m/s p=0.005), HR (p < 0.001), systolic (p < 0.015) and diastolic (p < 0.004) BP, waist circumference (p < 0.004), total and low density lipid cholesterol (respectively, 6.42 ± 1.41 vs. 5.89 ± 1.32, p=0.003 and 4.2 ± 1.18 vs. 3.8 ± 1.21, p = 0.002), and an increase in aerobic capacity (p < 0.001). In the control group there was no statistically significant changes of arterial stiffness parameters. Multivariate analysis revealed that reduction of arterial stiffness was BP-dependent. CONCLUSIONS In subjects with metabolic syndrome, HR targeted exercise training is associated with BP dependent decrease in aortic stiffness and improvement of metabolic and fitness parameters.