We hypothesized that there would be no difference in apparent absorption, as assessed by urinary excretion, between isoflavone sources rich in glucosides or aglucons and that subjects with rapid gut transit time (GTT) and low fecal isoflavone degradation phenotype would absorb more isoflavones. Women (n = 13) with a fecal daidzein degradation rate constant, D(k) > 0.30 h(-1) (high degraders) and GTT of 106 +/- 11 h and women (n = 12) with D(k) < 0.20 h(-1) (low degraders) and GTT of 71 +/- 12 h were randomly assigned to 3 treatments: soygerm (1.1 micromol/kg body weight, n = 5 high degraders, 4 low degraders), fermented soygerm (3.3 micromol/kg, n = 4 high and 4 low degraders) or Novasoy isoflavone extract (1.5 micromol/kg, n = 4 high and 4 low degraders) for 7 d. By HPLC analysis, 24-h urinary excretion of soygerm was greater than Novasoy (51 +/- 6 vs. 26 +/- 6% of ingested dose, P < 0.05). Women of the low daidzein degradation phenotype had greater urinary isoflavone excretion than did women of the high daidzein degradation phenotype (51.6 +/- 4.8 vs. 33.8 +/- 4.7%, P < 0.05, mean of d1 and 7). The plasma total isoflavone level (estimated as a percentage of the ingested amount, mean of d 1 and 7) differed between women who consumed fermented soygerm and soygerm 3 h after feeding (1.8 +/- 0.3 vs. 0.5 +/- 0.3%, P < 0.05). Urinary excretions of aglucons and glucosides did not differ. The study confirmed that rapid GTT and low fecal isoflavone degradation rate increased the apparent absorption of isoflavones.