Impediment of the promotion and progression stages of carcinogenesis of the prostate could have a profound impact on treatment choice and prognosis for prostate cancer. Efficacious chemopreventive agents that elicit their activity by slowing the processes of progression could make watchful waiting a viable alternative for a large population of men or could delay the necessity for surgery, radiation or other more invasive treatment modalities associated with frequent side effects. Reports from the Nutritional Prevention of Cancer (NPC) study reported that dietary supplementation with selenium significantly reduced the risk of developing prostate cancer. These data led to initiation of the Watchful Waiting Study, a phase II, multi-center, randomized, double-blind, placebo-controlled clinical intervention study testing the effects of two doses of selenized yeast on progression of prostate cancer. Participants are men with biopsy-proven prostate cancer who have elected to forgo therapy and be closely followed by ‘watchful waiting’ that includes quarterly prostate-specific antigen (PSA) screening. Subjects are randomized to receive 200 or 800 μg of selenized yeast or matched placebo daily. Endpoints include time to disease progression and PSA velocity. Secondary endpoints include time to initiation of therapy as well as biochemical markers of disease progression including chromagranin A and alkaline phosphatase. Immunohistochemical analyses for indicators of apoptosis, proliferation and differentiation will be performed on baseline and subsequent prostate biopsy specimens. This report summarizes the primary objectives, research methods and the randomized subjects in this important clinical trial.