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This paper presents how to model and carry out the performance analysis of message-oriented middleware (MOM) using generalised stochastic Petri Net (GSPN) models. The results obtained from the Petri net analysis are compared against ones measured in a commercial MOM. Additionally, some results are presented in order to demonstrate the flexibility and the benefits of the proposed model. This research also focuses on how to improve the MOM performance by suggesting appropriated techniques and adjustments to the MOM basic architecture. Finally, we point out some decisions usually taken by systems administrators that may have a major impact on the performance of MOM systems.