I have autoimmune thyroiditis. There have been some studies that show that soy may make thyroid problems worse and also interfere with thyroid medication. I do eat tofu and other soy products, but try to get most of my protein from other sources like beans, grains, and seitan. You are supposed to take thyroid medication on an empty stomach and not within four hours of soy products (I read that somewhere, sorry, I don't remember where). So I take my thyroid medication in the middle of the night (when I get up to pee!).
There is a book by Julia Ross called The Diet Cure that has suggestions for thyroid problems. I know of someone who had great success with these suggestions. She was told she would have to have her thyroid removed and be on meds for life. I was told she now has "normal" thyroid function after following the guidelines in the book. I've just started reading it.
Dairy protein is a common source of thyroid troubles but other dietary factors exist as well. Some find improvements with the addition of sea vegetables, others can get better by avoiding dairy or soy or iodine. It is unfortunately very complicated and there are variables from patient to patient. The same appraoch doesn't work for everyone.
I recommend superhero. It is based on an ancient, Asian system and is well balanced. It is the best way to get auto immune disease like thyroiditis under control quickly and permanently.
When it does help, the results are quick and dramatic. It is a good way to start.
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