This paper presents a simulation aided approach for designing organizational structures in manufacturing systems. The approach is based on a detailed modeling and characterization of the forecasted order program, especially of elementary processes, activity networks and manufacturing orders. Under the use of the organization modeling system FORM, that has been developed at the ifab-Institute of Human and Industrial Engineering of the University of Karlsruhe, structuring strategies-e.g., a process-oriented strategy can be applied in order to design organizational structures in manufacturing systems in a flexible and efficient way. Following that, a dynamical analysis of the created manufacturing structures can be carried out with the simulation tool FEMOS, that has also been developed at the ifab-Institute. The evaluation module of FEMOS enables to measure the designed solutions with the help of logistical-e.g., lead time degree and organizational-e.g., degree of autonomy key data. This evaluation is the basis for the identification of effective manufacturing systems and also of improvement potentialities. Finally, a case study is presented in this paper designing and analyzing different organizational structures of a manufacturing system where gear boxes and robot grip arms were manufactured.