Dietary intake of soy protein is associated with reductions in plasma cholesterol. Isoflavones are thought to be active components of soy and responsible for the beneficial effects because of their structural similarities to estrogen. The purposes of this study were to determine if i) soy protein or a semipurified soy extract, rich in isoflavones, is responsible for improving the lipid profile and ii) altered intestinal cholesterol metabolism is one mechanism for hypocholesterolemic effects. Ovariectomized adult female cynomolgus monkeys (40) were assigned to groups fed diets containing i) casein-lactalbumin (CAS) ii) intact soy protein (SOY), iii) CAS plus an isoflavone-rich semipurified soy extract similar in isoflavone content as SOY (ISO) or iv) CAS plus conjugated equine estrogen (CEE) for 20 wk. Cholesterol absorption was determined using the fecal isotope ratio method. Bile acid excretion was measured using the 3alpha-hydroxysteroid dehydrogenase assay. The SOY group had significantly lower total- and VLDL + LDL-cholesterol compared to the other three groups and significantly higher HDL-cholesterol compared to the CAS and CEE groups. Cholesterol absorption was significantly lower in the SOY group compared to the other groups, but bile acid excretion was not significantly affected. The hypocholesterolemic effect of soy protein appears to be mediated in part by decreased cholesterol absorption. The semipurified soy extract, rich in isoflavones, added to casein protein did not have lipid-lowering effects. Other components of soy such as saponins, phytic acid or the amino acid composition may be involved in the hypocholesterolemic effects seen in this study.