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In paper are presented main knowledge from the area of logistics, enterprise logistics and production logistics. On the base of theoretical knowledge in second part of the paper are described experiences from the application of logistics and simulation in the area of flexible manufacturing system design. The paper also introduces an example application of logistic flow optimization of a real flexible manufacturing system in firm Rostocker Maschinenbau und Technologie GmbH & Co.KG. Project was realized selected workers of the Faculty of Manufacturing Technologies of TU of Košice (Slovakia) in cooperation with workers of University of Applied Sciences in Wildau (Germany).