In this study we evaluated the long-term effects of soy isoflavones on intermediate markers of cancer risk in the normal postmenopausal monkey breast and uterus. Ovariectomized female cynomolgus monkeys were randomized to receive one of three diets for 36 months: 1) isoflavone-depleted soy protein isolate (SPI−) (n = 57); 2) soy protein isolate with the equivalent of 129 mg/d isoflavones (SPI+) (n = 60); or 3) isoflavone-depleted soy protein isolate with conjugated equine estrogens at a dose scaled to approximate 0.625 mg/d in women (n = 62). End points included breast and uterine proliferation markers, sex steroid receptor expression, and serum estrogens. Epithelial proliferation and progesterone receptor expression in the breast and uterus were significantly higher in the conjugated equine estrogen group, compared with SPI+ and SPI− groups, whereas no significant differences were detected between the SPI+ and SPI− groups. SPI+ treatment resulted in significantly lower serum concentrations of estrone (P < 0.01) and estradiol (P < 0.05) vs. SPI−. Within the SPI+ group, serum isoflavone concentrations were inversely correlated with serum estrone and mammary glandular area. These findings suggest that high dietary levels of soy isoflavones do not stimulate breast or uterine proliferation in postmenopausal monkeys and may contribute to an estrogen profile associated with reduced breast cancer risk.