Factors influencing the fate and impact of hybrids between crop plants and their related species operate from the early zygote, through to plant establishment in different habitats, to their ability to form self-sustaining populations. Many of the classes of genes being introduced by modern methods of genetic modification are similar to those manipulated by conventional plant breeding. In assessing the impact of transgenes in hybrids between crops and related species, therefore, it is important to be informed about the consequences of hybridization between conventionally bred varieties and their relatives. Some transgenes will have novel effects (e.g. production of pharmaceutical substances or certain fatty acids) on plants, and are likely to need specific assessment studies to determine their impact on hybrids. This will be particularly important if there is the possibility of these transgenes becoming established in wild populations. Some recommendations for further research are outlined.