Investment decisions for manufacturing systems are primarily based on three characteristics: cost of purchase and operation, cycle time in connection with maximum capacity and achievable work piece quality. However, such considerations neglect another important criterion: the flexibility that allows a manufacturing system to adapt to future production requirements and structures. The major barrier in integrating flexibility into the decision-making process is the difficulty to measure and compare it due to upcoming production scenarios that are not ultimately definable. Therefore, this paper presents a methodical concept for the evaluation of manufacturing systems using real options in order to incorporate flexibility in the decisionmaking process.