Background: We evaluated the effect of soybean extracts on serum lipoprotein profile and cholesterol accumulation on the arterial walls. Objective and design: Sixty-four female Sprague-Dawley rats were randomly divided into eight groups. Soybean extracts were given to the rats via oral gavage every day for eight weeks, after which serum was collected. In the thoracic aorta, left carotid artery, and right iliac artery, we measured the lipoprotein fractions in the serum and the accumulation of free cholesterol and cholesteryl ester, which are predictors of subclinical atherosclerosis. Results: After eight weeks of a continuous soybean diet, only two groups showed a lipid-lowering effect (n-hexane extract for 200 mg/kg dose and ethyl acetate extract for 200 mg/kg dose). We found lower free cholesterol and cholesteryl ester accumulation in the aortas and iliac arterial walls only in these two groups. Conclusion: The results indicated that soybean extract intake leads to weight change and may influence lipid metabolism. The positive effects of the soybean diet involved not only serum lipids but also aortic wall cholesterol accumulation.