This randomized clinical trial was designed to assess the effects of dietary isoflavones on vascular reactivity, lipid levels, and markers of inflammation in post-menopausal women. Epidemiological studies have revealed that populations consuming large amounts of soy protein have lower cardiovascular morbidity and mortality. The benefits of soy protein may be due to its hypolipidemic effects; its anti-oxidant properties; its high content of L-arginine; and/or or its phytoestrogen content. Two putative mediators of the effects of soy protein are the isoflavones genistein and daidzein. Forty post-menopausal, hypercholesterolemic women who did not take estrogen replacement therapy were recruited for this study of isoflavone supplementation. Baseline flow-mediated vasodilation and response to nitroglycerin were measured, along with urinary isoflavone and nitrite/nitrate levels and serum lipids. After 6 weeks of 90 mg of isoflavones daily versus placebo, women receiving isoflavones demonstrated improved responsiveness to nitroglycerin, an assessment of endothelium-independent vasodilation, with an effect size (percentage points change from baseline) of 7.2 +/- 1.9 versus 1.2 +/- 1.3; p = 0.01. There was a trend towards improvement of flow-mediated vasodilation, which is an endothelium-dependent response (effect size: 3.4 +/- 2.0% versus -0.6 +/- 1.7%; p = 0.12). Lipid levels were unchanged after isoflavone treatment. In conclusion, dietary isoflavones may have cardiovascular benefit in the form of improved vascular reactivity, but not by lowering cholesterol, for women who do not take estrogen replacement therapy.