The conservation of natural areas gives rise to costs that are borne both by the inhabitants of the area affected and by government, and to benefits that are enjoyed not only by locals but also by the existing and future population as a whole. The appraisal of such costs and the identification of the agents who bear them provides a useful tool for efficient decision-making, to support funding demands made on other levels of government, at both national and international level, and for the adoption of measures to compensate agents for rights. This paper describes a methodology for the calculation of such costs and presents the results obtained from its application in three areas forming part of the Natura 2000 network in Spain. Copyright © 2005 John Wiley & Sons, Ltd and ERP Environment.