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An analysis of the transportation systems used in the flexible manufacturing systems is introduced in the paper. Based on the analysis a class of the transportation systems is delimited, whose modeling and control is the subject of the paper. Important property of those systems is unidirectional zone movements of the automatic guided vehicles and transport requirements occurring spontaneously during the work of the system. A special group of the colored Petri nets interpreted for control is used for the control specification. The Petri net helps to analyze the function of the transportation system and to write the control program.