Consumption of soy protein is associated with a lower risk of cardiovascular disease in man, and reduced atherosclerosis in a variety of experimental animals. Although a portion of the cardiovascular protective effects appears to be due to reductions in plasma lipoprotein concentration, in most people the magnitude of this effect is relatively small. In many, but not all studies using animal models, the reduction in atherosclerosis is in part independent of changes in plasma lipids and lipoproteins. This implies that there may be a direct effect on the arterial wall of one or more of the components in soy protein that reduces susceptibility to atherosclerosis. The most actively studied components of soy protein that may be responsible for these anti-atherogenic effects are the isoflavones and various protein factions. Extraction of isoflavones and other alcohol-soluble components from soy protein lowers, but does not eliminate its ability to reduce atherosclerosis. Surprisingly, in most studies, adding back the isoflavone-rich alcohol extract to the previously extracted soy protein, or to another protein, does not restore its lipoprotein lowering or anti-atherogenic properties. This implies that alcohol extraction either destroys an active component of soy, alters the structural integrity of the soy proteins, or disassociates a required isoflavone—soy protein complex. Understanding the mechanism of this effect is an important goal for future research. Likewise, the sites of action on the arterial wall, and the mechanisms by 302 R. St. Clair and M. Anthony which various soy components act to reduce atherosclerosis are just now being studied. The recent demonstration that expression of estrogen receptor alpha is required for atheroprotection by soy protein provides important new mechanistic insight. Other properties of soy, including antioxidant, anti-inflammatory and potentially antithrombogenic properties need to be explored more mechanistically before the full potential of dietary soy protein for the protection from cardiovascular disease will be known.