Following the results of the Women's Health Initiative, many women now decline estrogen replacement at the time of menopause and seek natural remedies that would treat menopausal symptoms and prevent bone loss and other long-term consequences of estrogen deficiency, but without adverse effects on the breast, uterus, and cardiovascular system. The results of most soy studies in this population have had limitations because of poor design, small sample size, or short duration. This report describes the study rationale, design, and procedures of the Soy Phytoestrogens As Replacement Estrogen (SPARE) study, which was designed to determine the efficacy of soy isoflavones in preventing spinal bone loss and menopausal symptoms in the initial years of menopause. Women ages 45 to 60 without osteoporosis and within 5 years from menopause were randomized to receive soy isoflavones 200mg daily or placebo for 2 years. Participants have yearly measurements of spine and hip bone density, urinary phytoestrogens, and serum lipids, thyroid stimulating hormone, and estradiol. Menopausal symptoms, mood changes, depression, and quality of life are assessed annually. The SPARE study recruited 283 women, 66.1% were Hispanic white. With a large cohort, long duration, and large isoflavone dose, this trial will provide important, relevant, and currently unavailable information on the benefits of purified soy isoflavones in the prevention of bone loss and menopausal symptoms in the first 5 years of menopause. Given the high proportion of Hispanics participating in the study, the results of this trial will also be applicable to this minority group.