In this paper, four different physical treatments (microwaves, heating by conduction, sonication and pressure autoclaving) were performed to degrade a pure DNA extract, and their influence on GMO quantification was studied. The aim was to check the hypothesis that processing of agrofood products results in a similar degradation rate for both the transgenic target and the specific target. Indeed we could observe that even if the used physical treatments could lead to a significant increase of C _t values for both transgenic and specific targets, the resulting ΔC _t remained stable. So, the main conclusion of the study is that the aforementioned hypothesis seems valid and thus a physical degradation of DNA will not affect the relative quantitation of the GMO content, provided that both the specific and transgenic targets have very similar size. A second important issue of the experiments performed was that DNA is a very robust molecule as it is extremely difficult to reach a mean size below 100 bp. The study also gives evidence of the importance of using small targets.