BACKGROUND: The long-term clinical effects of soy protein containing various concentrations of isoflavones on endogenous hormones are unknown. OBJECTIVE: We examined the effects of ingestion of soy protein containing various concentrations of isoflavones on hormone values in postmenopausal women. DESIGN: Seventy-three hypercholesterolemic, free-living, postmenopausal women participated in a 6-mo double-blind trial in which 40 g protein as part of a National Cholesterol Education Program Step I diet was provided as casein from nonfat dry milk (control), isolated soy protein (ISP) containing 56 mg isoflavones (ISP56), or ISP containing 90 mg isoflavones (ISP90). Endogenous hormone concentrations were measured at baseline and at 3 and 6 mo. RESULTS: The concentration of thyroxine and the free thyroxine index were higher in the ISP56 group, and the concentration of thyroid-stimulating hormone was higher in the ISP90 group than in the control group at 3 and 6 mo (P < 0.05). Triiodothyronine was significantly higher in the ISP90 group only at 6 mo. Thyroxine, free thyroxine index, and thyroid-stimulating hormone at 6 mo were inversely associated with measures of baseline estrogenicity. No significant differences were found for endogenous estrogens, cortisol, dehydroepiandrosterone sulfate, insulin, glucagon, or follicle-stimulating hormone after baseline hormone values were controlled for. CONCLUSIONS: This study does not provide evidence that long-term ingestion of soy protein alters steroid hormone values, but it suggests that soy protein may have small effects on thyroid hormone values that are unlikely to be clinically important. The thyroid effects are, however, consistent with previous findings in animals and highlight the need for future research investigating possible mechanisms of action.