Soy products and cooked soybeans are safe at a wide range of intakes. However, a small percentage of people have allergies to soybeans and thus should avoid soy products.

Soy isoflavones have been reported to reduce thyroid function in some people.⁶ A preliminary trial of soy supplementation among healthy Japanese, found that 30 grams (about one ounce) per day of soybeans for three months, led to a slight reduction in the hormone that stimulates the thyroid gland.⁷ Some participants complained of malaise, constipation, sleepiness, and even goiter. These symptoms resolved within a month of discontinuing soy supplements. However, a variety of soy products have been shown to either cause an increase in thyroid function⁸ or produce no change in thyroid function.⁹ The clinical importance of interactions between soy and thyroid function remains unclear. However, in infants with congenital hypothyroidism, soy formula must not be added, nor removed from the diet, without consultation with a physician, because ingestion of soy may interfere with the absorption of thyroid medication.¹⁰

Most research, including animal studies, report anticancer effects of soy extracts,¹¹ though occasional animal studies have reported cancer-enhancing effects.¹² The findings of several recent studies suggest that consuming soy might, under some circumstances, increase the risk of breast cancer. When ovaries have been removed from animals—a situation related to the condition of women who have had a total hysterectomy—dietary genistein has been reported to increase the proliferation of breast cancer cells.¹³ When pregnant rats were given genistein injections, their female offspring were reported to be at greater risk of breast cancer.¹⁴ Although premenopausal women have shown decreases in estrogen levels in response to soy,^{15, 16} pro-estrogenic effects have also been reported.¹⁷ When pre-menopausal women were given soy isoflavones, an increase in breast secretions resulted—an effect thought to elevate the risk of breast cancer.¹⁸ In yet another trial, healthy breast cells from women previously given soy supplements containing isoflavones showed an increase in proliferation rates—an effect that might also increase the risk of breast cancer.¹⁹

Of 154 healthy postmenopausal women who received 150 mg of soy isoflavones per day for five years, 3.9% developed an abnormal proliferation of the tissue that lines the uterus (endometrial hyperplasia). In contrast, none of 144 women who received a placebo developed uterine hyperplasia.²⁰ Although no case of uterine cancer was diagnosed during the study, endometrial hyperplasia is a potential forerunner of uterine cancer. The amount of isoflavones used in this study is two to three times as much as that used in many other studies. Nevertheless, the possibility exists that long-term use of isoflavones could cause uterine hyperplasia, and women taking isoflavones should be monitored appropriately by their doctor.

Some postmenopausal women taking the soy isoflavone genistein have experienced gastrointestinal side effects (abdominal pain, epigastric pain, dyspepsia, vomiting, or constipation).²¹