Genetic modification could transfer allergenic properties from a donor organism into the recipient organism.  For example, if a potato has been modified using the gene of a peanut, a person is allergic to peanuts may also have an allergic reaction to the potato, even if they normally would not.  This is because the gene that is being transferred to the potato from the peanut contains whatever it is that the person is allergic to.

        The FDA does require food companies to demonstrate through scientific data that potential allergens are not contained in any of their GM foods, and if they are, the FDA requires a label indicating that fact.  Although the US regulatory agencies, FDA and EPA, require biotech companies to report presence of problem proteins in their modified foods (foods that may result in an unexpected allergy), there is a concern that unknown allergens can slip through the system.

        On the other hand, efforts are also underway to allergen free products, such as peanuts and rice.  People with allergies to these foods may one day be able to eat them, if scientists can alter the gene in the product that makes them allergenic.

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