Crops such as Bt cotton produce pesticides inside the plant. This kills or deters insects, saving the farmer from having to spray pesticides. The plants themselves are toxic, and not just to insects. Farmers in India, who let their sheep graze on Bt cotton plants after the harvest, saw thousands of sheep die!
Herbicide tolerance lets the farmer spray weed-killer directly on the crop without killing it. Comparative studies on the toxic residues in foods from such crops have not yet been done.
Pollen from GM crops can contaminate nearby crops of the same type, except for soy, which does not cross-pollinate. In fact, virtually all heritage varieties of corn in Mexico (the origin of all corn) have been found to have some contamination. Canola and cotton also cross-pollinate.