Looking back over the five years since a similar review of the field, this paper considers some of the research designed to address those uncertainties that, in part, led to the delay in the commercial-scale release of genetically modified (GM) crops in the UK. This research has included studies of the impact of transgenes on crop biology and invasiveness, the frequency and consequences of hybridisation between crops and their wild relatives and, in two costly large-scale investigations in the USA and UK respectively, attempts to assess the environmental impact of GM crops grown on a commercial scale. The first, on the effects of Bt corn on the Monarch butterfly, has important lessons for the risk assessment process. The second, farm-scale evaluations of GM herbicide-tolerant crops, should provide a blueprint for the management of the crops within an agricultural landscape delivering both food and biodiversity.