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This paper presents a generalized method for management decision making incorporating risk assessment techniques. The risk based decision making methodology is applied to European Union expenditure programs used to implement its regional policy, such as the community support framework, community initiatives, special initiatives and other European policies. An example is presented for the development of an audit (inspection) program in the region of West Macedonia, Greece, during the implementation of the 3rd Community Structural Support Framework Operational Program. The generic nature of the method permits its use in the management of similar European regional programs in Greece and other European countries. It is also applicable to many other industries interested in applying risk-based management decisions to physical or process based systems. .