Numerous analytical methods, both qualitative and quantitative, have been developed to determine reliably the presence and/or the amount of genetically modified organisms (GMOs) in agricultural commodities, in raw agricultural materials and in processed and refined ingredients. In addition to the 'classical' methods for DNA and protein analysis, e.g. polymerase chain reaction and enzyme linked immunosorbent analysis, certain types of GMO-containing matrices can be profiled by complementary chemical analysis methods such as chromatography and near infrared spectroscopy. This review summarises the status of the most widely used GMO analysis technologies, identifies new areas of analytical investigation and discusses current needs and future challenges.