How oral antibiotics (OABX) alter isoflavones (IFLs) in soy-consuming children is unknown. We evaluated OABX effects on urinary IFL excretion rates (UIERs) in 17 children, ages 4 to 17 yr, who provided 2 urine collections in pairs of a baseline urine and an overnight urine collection after consuming a body-weight-adjusted dose of soy nuts. The first collection was during OABX treatment for a bacterial infection and the second when healthy and off antibiotics. IFL food levels and UIERs were measured for nonmetabolites (NM), namely, daidzein, genistein (GE), and glycitein, and the metabolites (M) dihydrodaidzein, dihydrogenistein, equol, and O-desmethylangolensin (DMA), by liquid chromatography mass spectrometry. Urinary IFLs were hypothesized to change after OABX due to intestinal microflora alterations. A total of 11 children completed the study correctly. During OABX use, UIER (nmol/h/kg) for GE (6.4 ± 1.0 vs. 10.1 ± 1.6), all NM (27.5 ± 4.8 vs. 36.2 ± 4.7), and total IFLs (all NM + all M; 29.4 ± 5.0 vs. 38.8 ± 4.8) was reduced (P < 0.05) vs. when healthy. In contrast, a trend toward more DMA production during OABX was observed (1.2 ± 0.6 vs. 0.4 ± 0.3, P = 0.13). The reduction in urinary IFL appearance could be due to the changes of intestinal bacteria by OABX and/or due to processes related to the infection.