In most of the important crops in the world, gene flow between cultivars and between wild and weedy relatives has always taken place. Factors influencing this gene flow, such as the mating system, mode of pollination, mode of seed dispersal and the particular characteristics of the habitat where the crops grow, are difficult to evaluate and in consequence, the quantification of gene flow is not easy. Transgene flow from engineered crops to other cultivars or to their wild and weedy relatives is one of the major concerns in relation to the ecological risks associated with the commercial release of transgenic plants. With transgenic crops it is important to quantify this gene flow and to try to establish strategies to control or minimise it, taking into account the possible ecological effect of the newly introduced genes, whether advantageous or disadvantageous. The use of transgenic plants has proven to be an effective tool to quantify the gene flow to other cultivars of the same species or to wild and weedy relatives in all crops analysed. Here we review the major studies in this area, and conclude that the potential risk of gene flow has to be assessed case by case and caution is necessary when making general conclusions.