The labelling of genetically modified organisms (GMOs) is mandatory in the EU. To comply with this regulation, the International Standardisation Organisation recently published standards for the extraction of DNA and PCR detection of GMOs. The PCR detection of (GM) soy lecithin in chocolate however is not an easy assignment. For the most part this is due to inhibitors such as polyphenols resulting from the cocoa mass and the low level of soy lecithin present. Many factors however, such as the choice of extraction method, sample size and PCR protocol influence the PCR end result. Therefore, preconditions regarding the quality, quantity and purity of the extracted DNA should be carefully determined to guarantee a successful GMO analysis.