Objective: To assess the effect of phytoestrogens on bone turnover and growth in adolescent boys. Design: Randomized double-blind placebo-controlled trial. Setting: Single school in northwest Tasmania. Participants: Adolescent boys (treatment n = 69, placebo n = 59, mean age 16.8 y). Interventions: Six weeks of isoflavone supplementation (Novasoy, 50 mg daily of isoflavone equivalents). Bone turnover markers (bone specific alkaline phosphatase (BAP) and pyridinoline creatinine ratio (PYR)) were measured at baseline and follow-up. Results: Despite marked increases in urinary genistein and daidzein in the treatment arm (both P < 0.001), there were no significant differences in BAP, PYR or short-term height or weight change. This applied to both intention-to-treat and per protocol analysis. Neither was there a significant correlation between urinary genistein and daidzein levels and BAP or PYR. Conclusions: Phytoestrogen supplementation to the level of usual Japanese dietary intake has no measurable effect on bone turnover in adolescent boys. Longer-term studies of bone density may be desirable but it is unlikely that there will be a large effect in either girls or boys given the lower endogenous oestrogen levels in boys.