The Human Genome Project took about 13 years and cost millions of dollars and considerable effort to be completed in 2003. The advent of Next Generation Sequencing (NGS) technologies in the period 2004-2006 provided a new and incredible impulse to research. In fact, compared to standard classical DNA sequencing (Sanger), NGS allows the reading of DNA on a massive scale and for little cost. Only in the last five years has NGS been applied for characterisation of genetically engineered (GE) crops, maybe because NGS has only recently become more precise and cheap. An overview of the possible applications is explained.