The consumption of isoflavone-containing foods such as soybean and soybean products has been reported to have beneficial effects on the cardiovascular system in postmenopausal women. The present study was carried out to examine the mechanism underlying the beneficial effects of isoflavones in apolipoprotein (apo) E-deficient mice subjected to ovarian resection. Compared with sham-operated mice, ovariectomized mice had a larger arterial lesion area in the aortic root. Feeding the ovariectomized mice an isoflavone-containing diet (0.055 mg/kJ of total isoflavones/cal of diet) reduced the size of these lesions more than did feeding them with an isoflavone-free diet. Neither ovariectomy nor diet had a significant effect on the concentration of cholesterol in serum and urinary levels of isoprostanes, which are biomarkers for oxidative stress in vivo. The ovariectomized mice showed a greater increase in mRNA abundance for monocyte chemoattractant protein (MCP)-I in the aorta and in the level of nitric oxide (NO) secreted by peritoneal macrophages in culture than did the sham-operated mice. The isoflavone-containing diet lowered the MCP-I expression and the NO secretion more than did the isoflavone-free diet. These results suggest that dietary isoflavones confer an antiatherogenic effect by preventing the activation of macrophages due to the removal of ovaries.