Majority (about 90%) of the food borne allergies are due to peanut, soybean, egg, fish, crustacean, wheat, tree nut and milk.  Now a days, the increased food demand has been met by the genetically modified (GM) foods by utilizing the modern biotechnological tools.  Although, earlier very little attention was paid on food allergy, the development of new varieties of GM crops have generated increased concern in this field and have tremendously raised the issue in public.  Despite numerous adverse effects of food allergens, adequate knowledge on food allergens/allergy and their assessment is yet to be achieved.  A number of protocols based on their characteristics such as the abundance of the novel protein in food, stability to digestion and heat and amino acid homology have been developed but none of these protocols can accurately assess the allergenic potential of foods or their components.