A significant number of allergens arise from foods. The allergic risk of transgenic foods must be evaluated in accordance with the recommendations of the Joint Expert Committee FAO/WHO. Potential issues are the risk of cross reactivity with existing allergens, the modification of allergenicity of the transgenic protein induced by a modified metabolism in the host, the modified allergenicity of the proteins of the transgenic plant, a potential neo-allergenicity of the transgenic protein, and the risk of dissemination through pollens, inducing a respiratory sensitization then a cross food allergy. The algorithm includes three steps for evaluation: first the search for significant homology of the protein with allergens listed in allergen databanks, or the identity of a sequence of six aminoacids with known epitopes, then a cross reactivity explored through the binding to IgEs from patients allergic to the source of the gene, or allergic to organisms of the same group or botanical family, and finally the extent of the pepsine resistance. The risk of immunogenicity has to be studied with appropriate animal models. A post-marketing surveillance is recommended for monitoring of adverse effects. The structure of an Allergo-Vigilance Network, the tools for efficiency and the groups at higher risk will be discussed. The potential risk of transgenic foods to be allergenic cannot be overlooked, not ignoring the fact that current technologies modify allergenicity of foods.