Postmenopausal women or ovariectomized rats are associated with increased cholesterol levels, which are risk factors of metabolic syndrome and cardiovascular diseases. Increased prevalence of metabolic syndrome after menopause might be associated with estradiol deficiency. Harmful effect of estradiol hampers the casual usage of hormone to prevent the metabolic syndrome. Soy protein has been reported to show several beneficial effects on health, however it is unclear which components of soy protein is responsible for anti-obesity and hypocholesterolemic effects. Soy isoflavones, gem-stein and daizein, are suggested to have anti-obesity and hypocholesterolemic effects but with inconsistency. The present study investigated the effect of supplementation of genistein (experiment I) and soy protein containing isoflavones (experiment II) to high fat diet on body weight gain, food intake, liver and fat tissue weight and the lipid levels in ovariectomized rats. Plasma and hepatic lipid contents and the mRNA levels of genes encoding lipid metabolism related proteins, such as CPT1 and HMGR were measured. Ovariectomy increased body weight, fat tissue weight and plasma and hepatic lipid levels which increase the risk of metabolic syndrome. Soy protein could improve plasma and hepatic lipids levels. Soy protein also increased hepatic CPT1 and HMGR mRNA levels. Plasma and hepatic lipids levels could not be decreased by dietary genistein alone. In contrast, lipids levels could be decreased by isoflavone-fortified soy protein, suggesting that the ingestion of soy protein enriched with isoflavone gives more benefit for protecting postmenopausal women from metabolic syndrome.