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There has been some concern that the phytoestrogens in soy formulas may interfere with the immune system, the thyroid, or with how the reproduction system develops.
Soybeans are high in phytoestrogens, which are estrogen-like compounds found in plants or plant products. The AAP says that there is no "conclusive evidence" from any animal, adult, or infant study showing that that eating soy causes problems to "human development, reproduction or endocrine function."
The AAP urges further study on soy-based formulas.
I used soy with my now adult children, and both have problems now that could be linked to the soy. My nephew also used soy, and he also has some problems that can be linked to soy formula.
Soy would not be my first "go to" formula.
http://www.webmd.com/parenting/baby/...th-soy-formula