The European Commission has published a Communication on the Precautionary Principle and a White Book on Governance. These provide us (as research civil servants of the Commission) an institutional framework for handling scientific information that is often incomplete, uncertain, and contested. But, although the Precautionary Principle is intuitively straightforward to understand, there is no agreed way of applying it to real decision-making. To meet this perceived need, researchers have proposed a vast number of taxonomies. These include ignorance auditing, type one-two-three errors, a combination of uncertainty and decision stakes through post-normal science and the plotting of ignorance of probabilities against ignorance of consequences. Any of these could be used to define a precautionary principle region inside a multidimensional space and to position an issue within that region. The role of anticipatory research is clearly critical but scientific input is only part of the picture. It is difficult to imagine an issue where the application of the Precautionary Principle would be non-contentious. From genetically-modified food to electro-smog, from climate change to hormone growth in meat, it is clear that: 1) risk and cost-benefit are only part of the picture; 2) there are ethical issues involved; 3) there is a plurality of interests and perspectives that are often in conflict; 4) there will be losers and winners whatever decision is made. Operationalization of the Precautionary Principle must preserve transparency. Only in this way will the incommensurable costs and benefits associated with different stakeholders be registered. A typical decision will include the following sorts of considerations: 1) the commercial interests of companies and the communities that depend on them; 2) the worldviews of those who might want a greener, less consumerist society and/or who believe in the sanctity of human or animal life; 3) potential benefits such as enabling the world's poor to improve farming; 4) risks such as pollution, gene-flow, or the effects of climate change. In this paper we will discuss the use of a combination of methods on which we have worked and that we consider useful to frame the debate and facilitate the dialogue among stakeholders on where and how to apply the Precautionary Principle.