In recent years, isoflavones have increased in popularity as an alternative to estrogen therapy, particularly after the Women's Health Initiative demonstrated an increased risk of breast cancer, stroke, and heart attacks in response to estrogen and progesterone intervention. Isoflavones are heterocyclic phenols with structural similarity to estradiol-17beta and selective estrogen receptor modulators. Actions at the cellular level depend on the target tissue, receptor status of the tissue, and the level of endogenous estrogen. Clinical studies of soy-based diets evaluating the relation between soy consumption and serum lipid concentrations revealed that soy consumption significantly decreased total cholesterol, low-density lipoprotein cholesterol, and triglyceride levels. Epidemiological studies suggest a protective effect of soy protein on breast tissue as evidenced by the lower rates of breast cancer in East Asian countries where soy is a predominant part of the diet. Soy products also alleviate menopausal symptoms by reducing hot flashes. However, whether these biological effects of soy products originated from isoflavones is not clear. Furthermore, data available from human studies on the effect of isoflavones on osteoporosis are limited, and additional studies are needed to support a role in osteoporosis prevention. To date, no adverse effects of short- or long-term use of soy proteins are known in humans, and the only adverse effects known are those reported in animals. In conclusion, isoflavones are biologically active compounds, and current data are insufficient to draw definitive conclusions regarding the use of isoflavones as an alternative to estrogen for hormone replacement in postmenopausal women. Large, long-term intervention studies examining adverse effects and disease outcomes are needed before definitive conclusion can be drawn.