The detection and exact quantification of the presence of GMOs (genetically modified organisms, also named as living modified organisms, LMOs) grains has become very important in international commercial transactions, especially from countries producing both types of commodities, GMOs and GMO-free. This makes necessary to check every batch previous delivery to the recipient country. Several PCR protocols have been proposed to detect the presence of GMO DNA in a sample due to its sensitivity and independence of environmental and physiological influences. However, most of them are qualitative assays and don't give a good quantitative estimation of the detected signal. We developed a semi-quantitative method based on the comparison of the mass of the amplification product of the sample with the mass obtained from standard samples of known GMO concentration delivering an accurate estimation of the amount of GMO in a sample. At the same time the reaction is countersigned by an internal reaction control. A strict set up of the conditions is essential to control error-prone steps (like the quantification of the DNA template and of the DNA products and pipetting errors) that may bias the result. Using this protocol, we were able to routinely assess the quantity of transgenic grains present in shipments that sum more than 600,000 tons of corn and 250,000 tons of soybean exported between 1997 and 1999.