The objective of the study was to determine the effect on bone density of a red clover-derived isoflavone supplement that provided a daily dose of 26 mg biochanin A, 16 mg formononetin, 1mg genistein and 0.5 mg daidzein for 1 year. The effects on biochemical markers of bone turnover and body composition were also studied. Women aged 49–65 years were enrolled in a double-blind, randomised, placebo-controlled trial; 177 completed the trial. Bone density, body composition, bone turnover markers and diet were measured at baseline and after 1 year. Loss of lumbar spine bone mineral content and bone mineral density was significantly lower in the women taking the isoflavone supplement than in those taking the placebo. There were no significant treatment effects on hip bone mineral content or bone mineral density, markers of bone resorption or body composition, but bone formation markers were significantly increased in the intervention group compared with placebo in post-menopausal women. Interactions between treatment group and menopausal status with respect to changes in other outcomes were not significant.