The goal of this study was to evaluate how oral antibiotics (OABX) change the appearance of isoflavones (IFLs) in adults and children after soy consumption. The urinary IFL excretion rate (UIER) known to reflect circulating IFLs was hypothesized to change due to intestinal microflora changes by OABX. Subjects provided urine collections in pairs of a baseline urine and an overnight urine before and after consuming soy nuts first during OABX treatment and then again when healthy. During OABX versus when healthy, UIER (nmol/h/kg) in adults (n = 12) was increased (P < 0.05) for daidzein (35.2 +/- 7.2 vs. 18.9 +/- 2.4), daidzein + genistein + glycitein [nonmetabolites (NM); 42.6 +/- 8.0 vs. 23.6 +/- 2.9), and total isoflavonoids (Total IFLs; daidzein + genistein + glycitein + dihydrodaidzein + dihydrogenistein + equol + O-desmethylangolensin) (51.5 +/- 10.3 versus 29.6 +/- 4.7). In contrast, children (n = 7) showed reduced UIER (P < 0.05) when on OABX versus when healthy for daidzein (36.3 +/- 6.4 vs. 46.8 +/- 4.7), dihydrodaidzein (1.2 +/- 0.6 vs. 3.0 +/-1.1), NM (46.3 +/- 8.2 vs. 59.5 +/- 6.0), dihydrodaidzein + dihydrogenistein + equol + O-desmethylangolensin (1.0 +/- 0.8 vs. 4.3 +/- 1.3), and Total IFLs (48.2 +/- 8.5 vs. 63.8 +/- 6.4).