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In the IEEE 802.16 the number of errors and the MAC PDU size have an impact on the performance of the network. We present a way to estimate the optimal PDU size and we run a number of simulation scenarios to study these parameters and how they impact on the performance of application protocols. The simulation results reveal that the channel bit error rate has a major impact on the optimal PDU size in the IEEE 802.16 networks. Also, the ARQ block rearrangement influences the performance.