Isoflavones are thought to have an important role in the prevention of hormone-related diseases. This study was undertaken to identify the profile of urinary isoflavone metabolites collected within 24 h after the consumption of unfermented or fermented soy foods. The proportions of β-glycosides and aglycones to total isoflavone intake were much higher in soybean paste than soy flour. Twenty urinary isoflavone metabolites were identified using LC(ESI)-MS/MS. After enzymatic hydrolysis, glucuronide forms of daidzein and genistein accounted for 76 and 86% of total isoflavones, demonstrating that the majority of urinary isoflavone metabolites are glucuronide conjugates. When comparing the areas under curves of two foods, total urinary isoflavones excretion was higher in subjects consuming soybean paste than in subjects consuming soy flour. Genistein glucuronides are cleared more slowly than daidzein glucuronides after soy consumption. These findings indicate that the bioavailability of isoflavones may be influenced depending on the chemical composition of soy isoflavones.