The purpose of the present study was to determine whether children experience a higher systemic exposure to isoflavonoids when consuming a body weight-adjusted dose of soya compared with adults. Forty study participants were recruited from a local Waldorf school, including twenty-one children and nineteen adults. Participants collected a baseline urine sample and ate immediately thereafter a body weight-adjusted dose of soya nuts (15 g/54.4 kg equivalent to 0.615 (SD 0.036) mg total isoflavones/kg) followed by a 12 h urine collection. Nineteen children and eighteen adults completed the protocol correctly (fourteen child-parent pairs). Children, compared with adults, showed a statistically significant (P < 0.05 by unpaired t test) higher urinary isoflavone excretion rate for daidzein (+39%), genistein (+44%), all non-metabolites (daidzein + genistein + glycitein; +41%) and total isoflavonoids (+32%). Isoflavones are more bioavailable in children v. adults. Urine is an excellent medium to determine systemic isoflavone exposure in children due to its non-invasiveness and high compliance, in particular when collected overnight; it also allows evaluation of completeness of specimen collection.