The state of the art of scientific and technical aspects of GMO analysis has significantly evolved during the last decade. This includes not only developments such as Next-Generation Sequencing (NGS) and digital PCR, but also challenges that derive from the application of New Genomic Techniques. In the spirit of the ‘1st Global Conference on GMO Analysis’ held in 2008 in Italy , these new trends and developments call for an update of scientific exchange within the international community of GMO detection.