The safety of food produced from genetically engineered (GE) crops is assessed for potential risks of food allergy on the basis of an international consensus guideline outlined by the Codex Alimentarius Commission (2003). The assessment focuses on evaluation of the potential allergenicity of the newly expressed protein(s) as the primary potential risk using a process that markedly limits risks to allergic consumers. However, Codex also recommended evaluating a second concern, potential increases in endogenous allergens of commonly allergenic food crops that might occur due to insertion of the gene. Unfortunately, potential risks and natural variation of endogenous allergens in non-GE varieties are not understood, and risks from increases have not been demonstrated. Because regulatory approvals in some countries are delayed due to increasing demands for measuring endogenous allergens, we present a review of the potential risks of food allergy, risk management for food allergy, and test methods that may be used in these evaluations. We also present new data from our laboratory studies on the variation of the allergenic lipid transfer protein in non-GE maize hybrids as well as data from two studies of endogenous allergen comparisons for three GE soybean lines, their nearest genetic soy lines, and other commercial lines. We conclude that scientifically based limits of acceptable variation cannot been established without an understanding of natural variation in non-GE crops. Furthermore, the risks from increased allergen expression are minimal as the risk management strategy for food allergy is for allergic individuals to avoid consuming any food containing their allergenic source, regardless of the crop variety.