The EFSA ANS Panel was asked to deliver a scientific opinion on the possible association between the intake of isoflavones from food supplements and harmful effects on mammary gland, uterus and thyroid in peri- and post-menopausal women. Isoflavones are naturally occurring substances which can be found in, among other sources, soy, red clover and kudzu root. The main isoflavones are genistein, daidzein, glycitein, formononetin, biochanin A and puerarin. Their chemical structures are related to 17β-oestradiol and they possess oestrogenic properties. Furthermore, isoflavones may interact with the synthesis of thyroid hormone. Food supplements targeted at peri- and post-menopausal women typically provide a daily dose of isoflavones in the range of 35–150 mg/day. A systematic review was performed to investigate whether an association could be found between intake of isoflavones from food supplements and adverse effects on the three target organs in peri- and post-menopausal women. The human data did not support the hypothesis of an increased risk of breast cancer from observational studies nor of an effect on mammographic density nor on proliferation marker Ki-67 expression in interventional studies. No effect was found on endometrial thickness and histopathological changes in the uterus up to 30 months of supplementation with 150 mg/day of soy isoflavones. After 60 months some non-malignant histopathological changes were reported. Thyroid hormones levels were not changed following intake of isoflavones from food supplements. The background exposure from the diet in the general European population was estimated to be lower than 1 mg/day, whereas in consumers of soy-based foods it could be higher. The Panel concluded that it was not possible to derive a single health-based guidance value for the different preparations in post-menopausal women. However the doses used in the intervention studies and their duration could serve as guidance for the intake of food supplements.