The relative contribution of the small intestine to absorption and microbial metabolism of ingested isoflavonoids (IFN) was investigated in swine with canulae in distal ilea to facilitate collection of chyme (canula open). Weaned swine were fed a single meal containing ground roasted soybean and corn with canulae open followed by a second test soy diet at 48 h with canulae closed to allow passage of chyme into the large intestine. All remaining feedings were soy-free (corn–casein diet). Ileal effluent and urine were collected for 16 and 48 h, respectively, and analyzed for IFN and microbial metabolites of IFN. IFN in ileal effluent were present entirely as aglycones. IFN equivalents excreted for 24 h after ingesting the soy diet were not significantly different when canulae were open or closed. Urinary IFN aglycone equivalents on day 2 were similar to those on day 1 when canulae remained closed, but less than 10% of that on day 1 when canulae were open for 16 h postfeeding. Urinary concentrations of dihydrodaidzein, dihydrogenistein, O-desmethylangolensin, and equol exceeded IFN aglycone equivalents. These findings suggest extensive preabsorptive conversion of IFN glucosides to aglycones in the small intestine and relatively efficient microbial metabolism of IFN in weaned swine.