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The paper presents a prototypical implementation of a Java thread-based run-time environment for IEC 61499 applications and its use in the application design process. In particular, the paper focuses on the features of the developed environment and on its advantages and disadvantages. The purpose of this work is also to show the potentialities and the limitations of the IEC 61499 models in practical utilization. The described run-time environment has been tested for different application examples for both discrete manufacturing systems and motion control problems.