Ovarian hormone deficiency is a major risk factor for osteoporosis. Current therapies emphasize the use of antiresorptive agents, such as estrogen, calcitonin, and bisphosphonates. These therapies are associated with certain risks and side effects making compliance a major obstacle. Recent findings suggest that a class of synthetic and naturally occurring compounds, selective estrogen receptor modulators, e.g. raloxifene and soy isoflavones can offer attractive alternatives. Evidence for bone-sparing effects of isoflavones relies mainly on animal findings supported by a limited number of human studies. These observations suggest that isoflavones exert their effects on bone by stimulating bone formation and at the same time suppressing bone resorption. However, the precise osteoprotective mechanism of isoflavones remains uncertain and awaiting further clarification. From a clinical point of view, larger and longer duration studies are warranted to enable us to draw clear conclusions in regards to the role of isoflavones on bone.