Abstract: The present report summarises the bioinformatics analyses performed by the European Union Reference Laboratory for Genetically Modified Food and Feed (EURL GMFF) on the reference genes commonly used for detecting GM events in maize, soybean, cotton and rapeseed. The analysis had two objectives: first, to estimate the copy number of these genes in the available genomes of these species to ensure their low and constant copy number in the varieties possibly present on the market; second, to predict expected and unexpected amplifications using in silico PCR simulations to verify the specificity of the related taxon-specific methods. In maize, the adh1 gene was found in three copies in one genome and in a single copy in all others. All of the copies are predicted to be amplified by the QT-TAX-ZM-001 method. In the same species, one copy of the hmg gene was found in all genomes, and is predicted to be amplified by the QT-TAX-ZM-002 method. In soybean, one copy of the le1 gene was found in all genomes, and is predicted to be amplified by the QT-TAX-GM-002 and QT-TAX-GM-003 methods. In cotton, two copies of the sah7 gene were found in all genomes; both copies are predicted to be amplified by the QT-TAX-GH-021 method. In the same species, two copies of the adhC gene were found in all genomes, however only one gene copy is predicted to be amplified by the QT-TAX-GH-019 method. In rapeseed, two copies of the fatA(A)gene were found in 5 out of 6 genomes, but only one gene copy is predicted to be amplified by the QT-TAX-BN-001 method. In the remaining genome, four copies of the fatA(A) gene were found, but only two of them are predicted to be amplified by the QT-TAX-BN-001 method.