Abstract Due to the market introduction of genetically modified crops (GMOs) as the Roundup Ready (RR) soya and Bt corn, the European food industry came face to face with the question of the use and labeling requirements on GMO crops and its derivatives. Although even today, no defined European legislation is available, a definitive need for detection methods exists. Both DNA and protein based methods have been developed and applied for the detection of RR soya beans and its derivatives. For the CP4 synthase, synthetic peptides corresponding with the antigenic and non-homologous parts of the CP4 synthase were synthesized and mono-specific anti-CP4 synthase monoclonal antibodies were prepared by hybridoma technology. The monoclonal antibodies were able to detect the CP4 synthase in the RR soya using Western blotting analysis. Detection limits were found between 0.5% and 1%. The method is currently validated for half-and final products. The applied DNA methodology was making use of polymerase chain reactions (PCR) using sets of primers along the gene encoding the Agrobacterium CP4 synthase. DNA extraction and purification conditions were examined on a case-by-case approach for a scala of soya products (lecithin, oil, soybean meal, soy protein isolates etc.), half-products and final consumer products. Detection limits were found between 0.01% and 0.1%. In this paper a comparison will be made between the two types of methods in relation to sample preparation, sensitivity, validation and the use for half-products and final consumer products.