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Could GM foods contain new toxins? All foods contain chemicals that are toxic or carcinogenic or both.  But it generally takes much more of a toxic compound than is present in food to cause a problem. There are exceptions to this rule, but over millenia, people have genetically altered the plants we use for food to decrease toxicity and enhance their utility as crops.  In some cases, people figured out how to reduce toxicity by cooking or some other treatment.  Nonetheless, plant breeding can also increase the abundance of a toxic compound. For example, two conventionally bred insect-resistant varieties of potato and celery turned out to have elevated concentrations of compounds that were toxic to humans, as well as to insects.  This happened because one of the ways plants protect themselves from insects and animals is by producing quite toxic chemicals. 

Today, however, our ability to analyze the complete chemical composition of a crop plant is quite good. Before a GM crop plant is introduced, the developer submits to the Food and Drug Administration (FDA) information that compares the chemical composition of the original variety with that of the modified variety The composition of the crop must be the same except for the addition or removal of the particular target protein which is being modified.  Moreover, a protein added to the food through introduction of a gene must be produced and tested for toxicity and analyzed for possible allergenicity.   This kind of analysis is only required for GM crops.  That means that GM foods are more thoroughly analyzed than any ever have been in human history.