Fourteen premenopausal women participated in a randomized, crossover controlled feeding study of three diets, each two menstrual cycles long. We compared a high saturated fat Western diet (control diet) with two other diets: the control diet plus soy protein (soy diet) and the control diet with polyunsaturated fat (PUFA diet) replacing most of the saturated fat. We measured reproductive and serum hormones, urinary estrogen metabolites and isoflavonoids, and menstrual cycle length. In the follicular phase, prolactin concentrations significantly decreased by 3.6 μg/dl (P = 0.047), follicle-stimulating hormone concentrations slightly increased by 0.1 IU/l (P = 0.076), and cortisol concentrations slightly decreased by 81.8 nmol/l (P = 0.088) with the PUFA diet vs. the control diet. The soy diet slightly increased menstrual cycle length by 1.8 ± 0.7 days (P = 0.088) and significantly increased (P < 0.0001) urinary isoflavonoid excretion. These well-controlled diets did not affect serum estrogens or urinary estrogen metabolites, suggesting that type of fat or consumption of soy with a high saturated fat diet may not alter breast cancer risk by these mechanisms.