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In order to strengthen research coordination and increase the effectiveness of investments, the Swiss Centre for International Agriculture (ZIL) embarked on a formal priority-setting exercise. The paper documents the decision-making process, examines the application of the analytic hierarchy process (AHP) as decision-support tool, and discusses the outcome of the process. Starting with a set of alternative research areas and potential decision criteria, the process went through several steps where necessary information was gathered and processed, criteria structured and weighted, and alternative research areas assessed against criteria. The AHP helped structure the multi-criteria decision problem, elicit criteria weights, and evaluate the expected contributions of the alternatives to the previously defined objectives. The outcome of the process was a prioritized list of potential research areas for ZIL's next programme phase. Sensitivity analysis was performed to test the stability of the priority ranking. The paper concludes with a discussion on the group decision-making process and an outlook onto the next steps towards a better focused research agenda of ZIL.