The objective of the study was to determine qualitatively by validated Real Time PCR method the occurrence of genetically modified maize and soybean in commercial food products from the Greek market. 70 independent samples were collected, including products from different categories (i.e. cereal based, biscuits and snacks) which declared either corn or soybean on the labelling. The result of the study indicated that 37.1% of maize and soy products (n=70) displayed in the Greek market have detectable levels of genetically modified maize or soy. These products were identified by specific primers and included common GMΟ detection primers for 35S and NOS terminator. Adequate repeatability and reproducibility was demonstrated for the applied Real Time PCR method, as evaluated by intra- and inter-laboratory tests.