Osteoporosis is characterized by reduced bone mass and structural deterioration of bone tissue leading to enhanced bone fragility and a consequent increase in fracture risk. Bone loss further increases in postmenopausal women when the ovaries stop making estrogens. Women undergoing treatment for osteoporosis require long-term dosing therapeutic regimens, that offer no symptomatic relief, and may cause side effects. To avoid this problem, many therapeutic alternatives have been proposed. Epidemiological data support a robust relationship between soy isoflavones, fracture incidence and bone mineral density in osteoporotic, postmenopausal women. These suggest that a high isoflavone intake, restores the metabolic balance of bone formation and resorption. However, this matter is still controversial and several reports show negative results, probably because different doses and/or isoflavones have been used. Although it is difficult to identify the specific isoflavone most involved in preventing or restoring bone loss, a review of current literature based on new encouraging preclinical and clinical data, indicates that aglycone genistein appears to be the most effective isoflavone in preserving bone health. Genistein aglycone, through a peculiar anti-osteoporotic dual mode of action, can positively regulate bone cell metabolism rebalancing bone turnover towards bone formation. Genistein in fact stimulates osteoblast and inhibits osteoclast function, mainly through the osteoprotegerin-sRANKL system. The positive results achieved by genistein aglycone intake, in terms of efficacy and safety, have stimulated the development of specially formulated medical food products for the clinical management of postmenopausal bone loss.