Isoflavones are disease protective components of soybeans. Isoflavone metabolism and bioavailability are key to understanding their biological effects. Isoflavone glucuronides, dominant biotransformation products in humans that are more hydrophilic than isoflavone aglycones, activate human natural killer cells in vitro but are less toxic to NK cells than the parent aglycones. Gut microbial isoflavone metabolites have also been identified, but remain to be well characterized. Gut transit time (GTT) seems to be a significant determinant of isoflavone bioavailability because women with more rapid GTT (<40 h) experienced 2-3-fold greater absorption of isoflavones than did women with longer GTT (>65 h). Isoflavone metabolism varies a great deal among individuals, thus limiting the quantitative value of urine or plasma isoflavones as biomarkers of soy ingestion. Defining and lessening interindividual variation in isoflavone bioavailability, and characterizing health-related effects of key isoflavone metabolites are likely to be crucial to further understanding of the health benefits of isoflavones.