We evaluated urinary isoflavonoid excretion as a biomarker of dietary isoflavone intake during two randomized soy trials (13-24 months) among 256 premenopausal women with a total of 1,385 repeated urine samples. Participants consumed a high-soy diet (2 servings/day) and a low-soy diet (<3 servings/week), completed 7 unannounced 24-hour dietary recalls, and donated repeated urine samples, which were analyzed for isoflavonoid excretion by liquid chromatography methods. We computed Spearman correlation coefficients and applied logistic regression to estimate the area under the curve. Median overall daily dietary isoflavone intakes at baseline, during low- and high-soy diet were 2.3, 0.2, and 60.4 mg aglycone equivalents, respectively. The corresponding urinary isoflavonoid excretion values were 0.4, 1.0, and 32.4 nmol/mg creatinine. Across diets, urinary isoflavonoid excretion was significantly associated with dietary isoflavone intake (rs=0.51, AUC=0.85; p<0.0001) but not within diet periods (rs=0.05-0.06, AUC=0.565-0.573). Urinary isoflavonoid excretion is an excellent biomarker to discriminate between low- and high-soy diets across populations, but the association with dietary isoflavone intake is weak when the range of soy intake is small.