There are studies which show that isoflavones may not be safe. These studies are mostly based on experiments with animals and studies in-vitro (where tests are done in cells grown in test tubes). The interpretation of these results and the extrapolations to humans is questionable. Most of the isoflavones dosages which were used are very high compared with normal usage.
A comprehensive review of the available scientific evidence by the FSA (European Food Safety Authority) has revealed no indication that isoflavones at levels typically found in food supplements cause harm to post-menopausal women .
Isoflavones can cause breast cancer
Isoflavones are similar in structures as human estrogen. Therefore it’s easy to make the theory that isoflavones are not safe for women with a cancer breast risk. Test with Raloxifene, a molecule similar to isoflavones, proved that they protect against breast cancer. Animal studies also show that fermented soyfood, miso or soy protein significantly improve the chemotherapeutic effects of Tamoxifen. In a in-vitro study the isoflavones genistein inhibited the growth of breast cancer cells. Genistein had a synergistic effect with tamoxifen. Based on the currently available evidence there’s no reason that consuming soy may cause breast cancer. With isoflavones supplements it’s easy to take too much isoflavones, which is not possible when consuming soyfoods. Not much data is available on the overconsumption of isoflavones supplements. It’s recommended not to consume more tan 50 mg isoflavones as supplement per day.
Isoflavones and infant development
In the United States, about 20 percent of the infants are given soy formulas. It has been suggested soy formula could accelerate puberty and cause developmental and reproductive abnormalities and thyroid disorders. Preliminary research in the US found that isoflavones of soy infant formula do not disrupt infant development, despite concerns from some scientists that the isoflavones could act like female hormones in infants. Studies at the Arkansas Children’s Nutrition Center have found no apparent long-term positive or negative effects of feeding infants soy versus cow’s milk formula. Ryowon C. et al investigated the effects of soy isoflavones on babies and concluded that soy-based formula could be used for long-term feeding of babies .
Adverse effects on boys or men
Because isoflavones are similar in structure than the ‘female’ hormone estrogen some people are very quick to make a link between isoflavones and development of breasts and adverse effect on fertility of boys and men. However, animal studies did not find any change in fertility. Studies on men taking isoflavones supplements showed no effect on plasma hormones or semen quality. Other studies showed no adverse effects on sperm quality in mice fed with genistein.
Isoflavones and thyroid
The hormones produced by the thyroid are needed for the growth. Soy appears to have potential effects involving the thyroid gland. Individuals with impaired thyroid function should discuss the intake of isoflavones with their phycisian because isoflavones have been observed to reduce absorption of thyroid medication. Studies have shown that infants fed with soy formula have the same development as infants fed with cow milk formula.
Studies showed that soyfoods, and their isoflavones, are associated with a reduced risk of thyroid cancer. Some studies hint that isoflavones may inhibit the function of the thyroid gland, though this inhibition may only be significant in individuals who are deficient in iodine. Therefore people who consume large amounts of soy or isoflavones should make sure that their intake of iodine is adequate.
Other studies on healthy humans have found that soy and isoflavones had no effect on thyroid hormone levels and actually increased levels in some cases.
 Isoflavones in food supplements for post-menopausal women: no evidence of harm. EFSA. October 2015.
 The long term effects of soy-based formula on isoflavone concentration of plasma and urine, and growth and recognition development at 10 and 20 months old infants. Asia Pac J Clin Nutr. 2004;13(Suppl):S123