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Agricultural researchers widely recognise the importance of sustainable agricultural production systems and the need to develop appropriate methods to measure sustainability at the farm level. Policymakers need accounting and evaluation tools to be able to assess the potential of sustainable production practices and to provide appropriate agro-environmental policy measures. Farmers are in search of sustainable management tools to cope with regulations and enhance efficiency. This study proposes an indicator-based framework to evaluate sustainability of farming systems. Main features of the indicators' framework are the relevance given to different spatial scales (farm, site and field), production and pedo-climatic factors, and a holistic view of the agro-ecosystem. The framework has been conceived to tackle different purposes ranging from detailed scientific analyses to farm-level management systems and cross-compliance. Agro-environmental indicators can be calculated, simulated with models or directly measured with different levels of detail proportionally to the aims of the evaluation exercise. The framework is organised in a number of environmental and production systems and sub-systems. For each system environmental critical points are identified with corresponding agro-environmental indicators and processing methods. A review of applications of the framework in Tuscany, Italy, since 1991 is presented. Applications range from prototyping farming systems, to integrated farm ecological-economic modelling, comparisons between organic, integrated and conventional farming systems, farm eco-management voluntary audit schemes and cross-compliance. Strengths and weaknesses of the framework are discussed against generic requirements of information systems and operational issues.