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A structured approach is discussed for analysing hierarchy in the organization of biological and physical systems. The need for a structured approach follows from the observation that many hierarchies in the literature apply conflicting hierarchy rules and include ill-defined systems. As an alternative, we suggest a framework that is based on the following analytical steps: determination of the succession stage of the universe, identification of a specific system as part of the universe, specification of external influences on a system¿s creation and analysis of a system¿s internal organization. At the end, the paper discusses practical implications of the proposed method for the analysis of system organization and hierarchy in biology, ecology and physics.