I have been concerned about soy for a number of years for several reasons and have recommended almost all of my clients stay off of soy. Soy, especially soy milk, has been marketed heavily as a healthy food when in fact it is not.
Soy has a depressive effect on thyroid function which it turn affects the rest of the hormone cascade over time. The likelihood that it is genetically modified (even when labeled organic) because of cross-contamination is also a concern.
The Archives of Internal Medicine reports that they hoped the plant form of estrogen found within soy would prevent bone loss and reduce menopause symptoms. This was not the case and they did not find a significant difference between study groups of women: one group ingested soy daily and one group took a placebo. And, the women who took soy isoflavone actually had more hot flashes.