Soy and their isoflavones (IFLs) are believed to protect against breast cancer, particularly when exposure occurs during childhood. Little is known about the bioavailability of IFLs in children and how this is affected by oral antibiotics (OABX). We measured IFLs by LC/MS and found that the urinary IFL excretion rate (UIER) reflects circulating IFLs accurately when area-under-curve (AUC) and identical time intervals are used (r=0.93; p<0.001). UIER in children and adults was determined when healthy and when on OABX by collecting urine in pairs of baseline and overnight specimen before and after consuming soy nuts, respectively. Compared to when healthy, children on OABX showed significantly decreased UIER but adults on OABX showed increased UIER (p<0.05). All 37 healthy children showed significantly higher UIERs compared to all 34 healthy adults. UIER is an adequate surrogate for determining IFL bioavailability and for measuring soy or IFL exposure in epidemiologic and other studies.