Mary Shomon: In researching my book, Living Well With Hypothyroidism: What Your Doctors Don’t Tell You…That You Need to Know, from HarperCollins, I talked to Dr. Mike Fitzpatrick, an environmental scientist and phytoestrogen researcher who has conducted in-depth studies on soy, particularly the use of soy formulas. Dr. Fitzpatrick makes it clear that soy products can have a detrimental affect on both adults and infants. In particular, he firmly believes that soy formula manufacturers should remove the isoflavones (that part of the soy products that act as anti-thyroid agents) from their products.
Researchers have identified that the isoflavones act as potent anti-thyroid agents, and are capable of suppressing thyroid function, and causing or worsening hypothyroidism. Soy is a phytoestrogen, and therefore acts in the body much like a hormone, so it’s no surprise that it interacts with the delicate balance of the thyroid’s hormonal systems. High consumption of soy products is also proven to cause goiter. 
Isoflavones belong to the flavonoid or bioflavonoid family of chemicals, and are considered endocrine disrupters — plants or other products that act as hormones, disrupting the endocrine system, and in some cases, this disruption involves acting as an anti-thyroid agent. (The grain millet, for example, contains high levels of flavonoids, and is commonly known as problematic for thyroid function). Flavonoids inhibit thyroid peroxidase (TPO), which disturbs proper thyroid function.
A feature on soy in the March 1999 issue of Natural Health magazine quoted Daniel R. Doerge, PhD, a researcher at the Food and Drug Administration’s National Center for Toxicological Research. Dr. Doerge has researched soy’s anti-thyroid properties, and has said
“ . . . I see substantial risks from taking soy supplements or eating huge amounts of soyfoods for their putative disease preventive value. There is definitely potential for interaction with the thyroid.”
One UK study of premenopausal women gave 60 grams of soy protein per day for one month. This was found to disrupt the menstrual cycle, with the effects of the isoflavones continuing for a full three months after stopping the soy in the diet. Isoflavones are also known to modify fertility and change sex hormone status. Isoflavones have been shown to have serious health effects — including infertility, thyroid disease or liver disease — on a number of mammals.
Infant Soy Formulas pose Particular Dangers
Mary Shomon: Since the late 1950’s, it has been known that soy formulas contain anti-thyroid agents. Infants on soy formula are particularly vulnerable to developing autoimmune thyroid disease when exposed to high exposure of isoflavones over time.  This study found that the frequency of feedings with soy-based milk formulas in early life was noticeably higher in children with autoimmune thyroid disease, and thyroid problems were almost triple in those soy formula-fed children compared to their siblings and healthy unrelated children. Dr. Fitzpatrick even believes that long-term feeding with soy formulas inhibits TPO to such an extent that long-term elevated TSH levels can also raise the risk of thyroid cancer.
Not much is being done in the U.S. to make parents aware of the thyroid-related dangers of soy formulas, or to alert the public that heavy soy consumption may be a danger to thyroid function. Other countries, however, are far ahead of the U.S. In July of 1996, the British Department of Health issued a warning that the phytoestrogens found in soy-based infant formulas could adversely affect infant health. The warning was clear, indicating that soy formula should only be given to babies on the advice of a health professional. They advised that babies who cannot be breastfed or who have allergies to other formulas be given alternatives to soy-based formulas.
Polly: Those warnings apply to toddlers too. Soy based milk substitutes meant for adults aren’t a good idea for children. Besides the isoflavones problem, they don’t supply enough vitamin D to prevent rickets. Rice milk is a problem for toddlers too. It doesn’t have enough protein in it to keep a child healthy.