This study was undertaken to determine the bioavailability of isoflavones in weanling Sprague-Dawley rats by providing diets containing different levels of soy isoflavones for 6 weeks: 0.025% (low isoflavone intake; LI), 0.125% (medium isoflavone intake; MI), and 0.25% (high isoflavone intake; HI). The subsequent fecal and urinary excretion of daidzein and genistein was then measured. As the levels of dietary isoflavones increased, the amount of food intakes significantly decreased, and weight gain was slower in female rats. In male rats, there was no significant difference in weight gains related to dietary intakes. Urinary excretion of daidzein and genistein was significantly higher in the MI and HI groups in both male and female rats than the control and LI groups. The recovery % of daidzein and genistein in the urine was significantly lower in the MI and HI groups. Fecal daidzein increased as dietary isoflavone intakes increased in female rats; however, in male rats the increase was significant only in the HI group. The recovery % of daidzein and genistein in the feces of female rats was not significantly different among the four groups. When dietary isoflavones were increased from 0.025% to 0.25%, the amounts of daidzein and genistein excreted in the urine and feces increased; however, the low recovery rate of both daidzein and genistein in the urine implies an increased bioavailability of isoflavones. We also observed sex-related differences in the urinary and fecal recovery of isoflavone intakes.