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Improvements in the welfare of farmed animals in the EU have been achieved by legislation, increased welfare capacity in the food chain, greater public awareness, welfare measurement tools and dissemination of best practice. However, pressure for improvement grows. The EC recognises that delivering improved welfare would best be achieved by increasing welfare capacity, including establishing a Network of Welfare Reference Centres to provide support for welfare research, knowledge transfer and policy design. Designing a structure for this Network presents a challenge, as it would have multiple functions, interact with diverse stakeholders and operate in a complex environment. Here, we describe the use of a novel strategic planning approach to design an optimal structure for this Network. Our evaluation found that no existing structure was ideal, but that by taking functional units from several existing models, an optimal model could be identified.