Sporadic intake and short half-lives of serum or urinary biomarkers may make serum and urinary isoflavones quite unreliable indicators of longer-term dietary soy intake. In 26 participants in the Adventist Health Study-2 (AHS-2) we obtained two measures of fasting morning serum isoflavones, 1-2 years apart. In another 76 subjects we obtained an overnight urine sample and six 24-h dietary recalls over a period encompassing the time of the urine sample. Intraclass correlations (ICC) values for serum isoflavones were 0.11 (log(daidzein)) and 0.28 (log(genistein)). Assuming that the correlation (true dietary intake, true urinary excretion) <0.90, it is shown that this implies an ICC for urinary estimates that exceeds 0.56. As expected, the previous day's soy intake, and its timing, influenced the next morning's serum levels. These results suggest that fasting morning serum isoflavone estimates will provide a poor index of long-term soy intake, but that overnight urinary estimates perform much better.