Cardiovascular disease (CVD) mortality rates are lower in Asian countries where dietary patterns are very different from Western diet. A number of studies have linked these lower rates to the inclusion of soy products as a staple food in those countries. Soy is the richest dietary source of isoflavones, a type of phytoestrogen associated with many potentially beneficial effects. Isoflavone-containing soy protein consumption has been linked to reduced levels of LDL cholesterol in hypercholesterolemic patients. This effect is increased with the concomitant administration of isoflavones, and seems to be also complemented by the isoflavone capacity to restore the endothelial function in patients with weak and moderated endothelial dysfunction. The effects are variable depending on individuals' metabolism and in particular to their ability to convert daidzein to equol that seems to be restricted to approximately 1/3 of the population. Equol production has been indeed linked to a decreased arterial stiffness and antiatherosclerotic effects via NO production. Because the relevance of isoflavones consumption on the modulation of cardiovascular risk still remains unclear, this paper aims to review the existing knowledge on the biological activity of the isoflavones on the human cardiovascular system from an epidemiological, clinical and -omics point of view.