Menopause is associated with an accelerated decline in vascular function, however, whether this is an effect of age and/or menopause and how exercise training may affect this decline remains unclear. We examined a range of molecular measures related to vascular function in matched pre- and post-menopausal women before and after 12 weeks of exercise training. Thirteen pre-menopausal and ten recently post-menopausal (1.6±0.3 (mean±SEM) years after final menstrual period) women only separated by three years (48±1 vs. 51±1 years) were included. Before training, diastolic blood pressure, soluble intercellular adhesion molecule-1 (sICAM-1) and skeletal muscle expression of thromboxane A synthase were higher in the post-menopausal women compared to the pre-menopausal women, all indicative of impaired vascular function. In both groups, exercise training lowered diastolic blood pressure, the levels of sICAM-1, soluble vascular adhesion molecule-1 (sVCAM-1), as well as plasma and skeletal muscle endothelin-1. The vasodilator prostacyclin tended (P=0.061) to be higher in plasma with training in the post-menopausal women only. These findings demonstrate that already within the first years after menopause, several biomarkers of vascular function are adversely altered, indicating that these biomarker changes are more related to hormonal changes than aging. Exercise training appears to have a positive impact on vascular function, as indicated by a marked improvement in the biomarker profile, in both pre- and post-menopausal women.