The TEEBAgriFood ‘Scientific and Economic Foundations’ report addresses the core theoretical issues and controversies underpinning the evaluation of the nexus between the agri-food sector, biodiversity and ecosystem services and externalities including human health impacts from agriculture on a global scale. It argues the need for a 'systems thinking' approach, draws out issues related to health, nutrition, equity and livelihoods, presents a Framework for evaluation and describes how it can be applied, and identifies theories and pathways for transformational change.