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The debate surrounding GMOs is a recurring one; it is unclear and often conveys the picture of a general brawl. Our article argues that this situation is linked to the crisis context in which we live, a modernity crisis in general and especially a rationality crisis. It tries to put some order in the sphere of debate and to contribute a clarification which avoids drifts and amalgamations that usually blight discussions. We propose to distinguish three levels of debate. The first is a purely scientific and technical debate concerning knowledge, in particular the assessment of risks. The second is political and deals with the merits of decisions to be taken, in particular regarding the application or non application of the precautionary principle. And the last involves a philosophical debate about values, in particular ideas about what “good life” is and about the relationships between man and nature. These distinctions justify that we consider a practical rationality, which we seek to define, alongside with theoretical rationality. Building a relevant practical rationality, not as a replacement but as a complement to theoretical rationality, is the first condition towards “civilizing” debates on GMOs. It is also a necessary step forward in the direction of participatory democracy, an imperative for the twenty-first century.