Sustainability is a key concept for our future and the role of thermodynamics in its assessment is fundamental. The use of energy and matter must be considered not only from a microscopic viewpoint (the use of a single fuel or material, or the presence of a single pollutant) but also by means of holistic approaches able to synthesize all the characteristics of a single process. Exergy is a suitable function for this purpose. The exergy concept can also be applied to natural systems and to systems at the interface between natural and artificial ones. In this context also emergy can express very helpful indications. Four different efficiency indices are here examined to better understand different aspects of the sustainability of processes and systems. An application to two similar agricultural systems (wine production in Italy) shows how these indices work in real case studies. Copyright (C) 2005 John Wiley Sons, Ltd.