Within the Genetically Modified Organism (GMO) regulatory framework, the safety assessment of GMOs involves the identification of the intended and unintended effects as a result of the genetic modification, a.o. through molecular characterisation. For most of the current transgenic crops the molecular characterisation consists of the determination of inserted DNA including the insert sequence, the insertion site(s), the number of inserts and its/their flanking regions. This is currently typically done by Southern blot (SB) and Polymerase chain reaction (PCR) analysis in combination with standard sequencing approaches. Next-generation sequencing (NGS) has had a profound impact on several areas of genomic research. Along with the diverse range of applications of NGS, some recent research projects and product developers explored the use of NGS as a tool for the molecular characterisation of GMOs in view of their risk assessment.