Taken from the weightloss board:
Regarding Soy
If you have thyroid imbalance or are female you may want to use whey protein rather than soy.
quote from:

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 are also proven to cause goiter, (Anti-thyroid isoflavones from soybean: isolation, characterization, and mechanisms of action, Divi RL; Chang HC; Doerge DR, National Center for Toxicological Research, Jefferson, AR 72079, USA, Biochem Pharmacol, 1997 Nov, 54:10, 1087-96)

Note: The best source of information on soy and its negative impact on health can be found at the Soy Online Service, and in particular, its page on phytoestrogenic effects of soy, and impact on the thyroid.

Isoflavones belong to the flavonoid or bioflavonoid family of chemicals, and are considered endocrine disruptors -- 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.

The March 1999 issue of Natural Health magazine has a feature on soy that quotes Daniel R. Doerge, Ph.D., a researcher at the Food and Drug Aministration'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.

Dr. Fitzpatrick believes that people with hypothyroidism should avoid soy products, because, "any inhibition of TPO will clearly work against anyone trying to correct an hypothyroid state." In addition, he believes that the current promotion of soy as a health food will result in an increase in thyroid disorders.