The potential environmental risks of cultivating transgenic crops have been the subject of much publicly funded research, which often seems to have increased controversy about transgenic crops, rather than assisted decision-makers. This stems from an ecological method of research that has several characteristics that limit its usefulness to decision-makers: a reluctance to define problems in relation to policy objectives; testing null hypotheses of no difference between transgenic and non-transgenic crops; a preference for detailed descriptions of ecosystem structure, complex models and precise predictions of uncertain relevance; and favouring tests of hypotheses under field conditions. A more effective method of research for decision-making follows principles exemplified by ecotoxicology: research problems are selected by policy relevance; testing of risk hypotheses that predict no harm of the transgenic plants to things of value; a preference for tests of ecosystem function, simple comparative models, and accurate and relevant, if qualitative, predictions; and favouring tests of hypotheses under conditions that provide most rigour. These principles may also be usefully applied to other environmental science research programmes that aim to inform decision-making.