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The complexity we take into account when dealing with complex issues and the way we deal with that complexity is not given or self-evident, it is framed and negotiated. Based on two environmental health decision support case studies we address a set of key methodological choices, crucial in shaping the multi-criteria decision support and illuminate how they followed from transdisciplinary collaboration and negotiation: diversity tolerance, dealing with uncertainty and difference of opinion, weight of information and the epistemological divide between traditional closed and alternative open paradigms. The case studies exemplify the growing conviction amongst methodologists that, especially regarding complex issues, best methods do not exist as such: methods are chosen and tailored in practice and the quality to a large extent is dependent on the process in which methodological development is embedded. We hope to contribute to making explicit the importance of methodological decision making regarding environmental health complexity.