Evaluating environmental impact is more complex than statistical analysis; it requires value judgements about which kinds of environmental impacts are acceptable and which are not. The new EU Directive on the release and commercialization of genetically modified (GM) crops (2001-18-EC) includes a requirement for an assessment of indirect effects on the environment of farming practices associated with the introduction of a GM crop. There is also a requirement for post-commercialization monitoring to address impacts of scale and time. Both of these additions to the regulations present challenges in deciding how environmental impacts should be measured, and in judging their acceptability. Impacts can also be socio-economic. These frequently require scientific tools to help to resolve them. The demands by some food sectors for zero GM content in crop produce is likely to prove difficult or impossible to verify by analytical procedures. It will probably be necessary to agree on levels of tolerance of the presence of GM material in “non-GM” crop produce. It is important that the future use of biotechnology in agriculture is considered in the context of a broader discussion about our vision for agriculture and the environment over the coming decades.