Sustainability evaluation has become a key component of international health. However, evaluators have faced a number of challenges linked to the lack of consensus on the meaning of the concept of "sustainability". This paper aims to describe a methodology, the Sustainability Analysis Process, based on several conceptual frameworks and tested in five different countries in the physical rehabilitation sector. The methodology consists of five successive steps: (i) overview of the context; (ii) system boundary; (iii) consensus vision of sustainability, and derivation of stakeholder perspectives; (iv) selection of sustainability indicators and characterization and analysis of local system sustainability; and (v) verification and modification. The paper also discusses the place of the evaluator and researcher in the process: the methodology aims to help evaluators objectively measure the level of sustainability of a health system with the challenge of dealing with a subjective notion, the concept of sustainability, and a diversity of actors. The Sustainability Analysis Process also aims to capture the dynamics of systems by repeating the process on a regular basis. The methodology highlights the need for evaluators build consensus amongst stakeholders on a common vision of the future of a health system.