The purpose of this phase I dose-finding randomized controlled trial was to evaluate the safe and effective dose of isoflavones to be used in future clinical trials for prostate cancer prevention. Forty-five eligible men were supplemented with 40, 60, and 80 mg of purified isoflavones or no supplement from biopsy to prostatectomy. Compliance with the study agent, toxicity, and changes in plasma isoflavones, serum steroid hormones, prostate-specific antigen (PSA), and tissue Ki-67 were analyzed from baseline to completion of the study. Forty-four subjects completed the study with a duration of intervention of 30 (+/- 3) days. We observed significant increases in plasma isoflavones with treatment for all doses compared with controls without producing any toxicity. Significant increases in serum total estradiol were observed in the 40 and 60 mg isoflavone-treated arms. However, a significant increase in serum free testosterone was observed in the 60 mg isoflavone-treated arm. Changes in serum sex hormone-binding globulin, PSA, and percentage of tissue Ki-67 were not statistically significant with treatment for this sample size and duration of intervention. Our results identify a safe dose of purified isoflavones for future clinical trials and establish the need for further definitive, well-powered trials to examine the role of isoflavones in prostate carcinogenesis.