From bottomlinefitness:

The vast majority of soy at your local market is not a health food. 91% of soy grown in the US is genetically modified (GM) soy that is contaminated with large pesticide residues. The genetic modification is done to impart resistance to the toxic herbicide Roundup, so they can spray it over the soy plants to improve crop production by killing the weeds. This is solely meant to increase farming efficiency and provide you with less expensive soy. In other words, cheap as opposed to healthy.
For centuries, contrary of what Americans have been told, Asian people have been consuming non-GM fermented soy products such as natto, tempeh, and soy sauce in SMALL amounts. Western food processors separate the soybean into two commodities—protein and oil. And there is nothing natural or safe about these products that many Americans consume.

Dr. Kaayla Daniel, author of The Whole Soy Story, points out thousands of studies linking soy to malnutrition, digestive distress, immune-system breakdown, thyroid dysfunction, cognitive decline, reproductive disorders and infertility—even cancer and heart disease.

Here is just a sampling of the health effects that have been linked to soy consumption:
* Breast cancer
* Brain damage
* Infant abnormalities
* Thyroid disorders
* Kidney stones
* Immune system impairment
* Severe, potentially fatal food allergies
* Impaired fertility
* Danger during pregnancy and nursing
Soy proponents will argue that soy-based foods (they lump the fermented ones with the unfermented) will protect you from everything from colon, prostate and breast cancer to strokes, osteoporosis, and asthma. However, proponents never mention the studies that illuminate soy’s downside and all of the dangers posed to your health, which are based on sound research.
Another unfortunate fact is that 80 percent of the world’s soy is used in farm animal feed, which is why soy production is contributing to deforestation. Some soy propagandists have suggested that the solution to this is for all of us to become vegetarians—a reckless recommendation rooted in total ignorance about nutrition—whereas a far better solution is a major overhaul in how farm animals are fed and raised.