Maize is one of the three most important crops in the world. It is used as feed, food, food ingredient and additive, and for industrial processing. Recently, its use as raw material for biofuels reaches 50% of the USA production. In addition to its economic importance, several maize lines were genetically engineered to express agriculturally desirable traits, including tolerance to pests and to herbicides, to increase crops productivity. Although, worldwide, several transgenic maize events may be cultivated, in European Union (EU), only one maize event is authorized for cultivation, the MON 810 event. Therefore, according to the European farmers’ freedom of choice between conventional, organic and GM crop cultivation, European guidelines were developed to help those Member States who intended to cultivate MON 810 maize, to develop either national laws or best practices to ensure coexistence between GM crops and conventional and organic farming. Although, in 2009, fifteen countries had already developed coexistence rules, the uncertain regulatory system concerning both plant-breeding methods, namely those creating GM crops bearing more than one transgene (stacked traits), and thresholds for the presence of adventitious GM seeds in conventional seed lots complicated maize seed trade. In EU, a maize variety having stacked events cannot be cultivated as coexistence only applies to GM crops bearing the single event authorized for cultivation. Besides, the adventitious presence of GM seed in conventional seed lots must meet the requirements of conventional maize growers and their customers The most used methods to screen for the presence of unauthorized maize events in seeds, based on real-time PCR, show many severe impediments. There is no certified reference material for the quantification of screening elements as for the P35S promoter or T-nos terminator; the detection limit of screening methods do not provide the information needed to ensure the absence of non-unauthorized GM seeds in conventional maize seed lots; there is no means to known if an event is stacked or not in ground seeds. We made a review of the situation in Portugal, both at the seed importation level and at the national grain production. We found that Nk603 maize is being stacked together with MON 810 as adventitious presences in conventional seed lots. Additionally, we found that analytical results may vary substantially among laboratories as many 3 producers request the quantification of GM material despite of the transgene identification. We compared results obtained with commercial Kits for the quantification of P35S with event-specific methods.