Food phytochemicals such as the polyphenolic flavonoids from a wide variety of foods and beverages have been associated with cardiovascular protective effects in epidemiologic studies. Significant controversy exists in the literature regarding the efficacy and mechanisms for the cardiovascular protection of soy foods. The soy hypothesis for cardiovascular risk reduction has been focused mainly on the isoflavone content of soy, but uncertainty still exists regarding the bioactive component(s). In particular, consumption of soy protein foods has been associated with favorable cardiovascular disease (CVD) risk profiles in population based studies. Controlled clinical trials and meta-analyses however, have resulted in the conclusions that soy protein with associated isoflavones has only modest hypocholesterolemic effects in the range of 3-5% reduction in LDL-cholesterol. Additional cardioprotective effects have been demonstrated in clinical trials, promoting small but significant changes in vascular endothelial function and antioxidant protection. An important observation is that animal studies have shown reduction in atherosclerotic lesion size both with and without decreased blood lipid levels. These results taken together suggest that soy and soy phytochemicals can promote positive risk factors and outcomes by mechanisms in addition to, and other than lowering serum cholesterol levels. There is a need for greater understanding of the cellular and molecular mechanisms underlying the physiologic responses to isoflavones in the vascular compartment. Increasing evidence is emerging that biologically relevant concentrations of isoflavones may impact cell signaling processes in vascular and other tissues.