The potential of genetically modified organisms (GMOs) to increase allergenicity or predispositions to allergies has attracted much attention. An approach that will properly and holistically evaluate the allergenicity of GMOs is yet to be found. Here, 85 transgenes that have been reported in both international and domestic studies during recent years are summarized case by case; 49 of the transformed genes were from plant sources and 36 were from animal sources. EVALLER™, a web server for the in silico assessment of potential protein allergenicity, was used to evaluate the potential of the transgenic proteins as allergens. The biomedical journals listed in Highwire (http://highwire.stanford.edu/) were searched and reviewed to decipher whether any of the transformed genes were linked to allergenicity or human health. The EVALLER analysis identified 5 allergenic genes, whilst our literature review found 11 genes that were either related to allergic cases or to clinical adverse events; all 16 of these genes have been used in GMOs. The analysis pathway that we have developed can help guide the selection of genes to be used in genetic modification. The pathway also provides a paradigm for allergenicity analysis of transgene candidates.