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This paper proposes a generalized approach for throughput analysis and demonstrates its application for performance evaluation in OCDMA networks. The proposed analysis approach takes into account not only the characteristics of the physical layer to support arbitrary BER models, but also the nodal architecture design at higher layers. In particular, we investigate the effects of packet corruption, channel collision, and destination contention on network performance, and obtain steady-state estimation for effective throughput. This throughput estimation sets a tight upper bound for achievable throughput in OCDMA networks with random access schemes. The proposed analytic approach leads to results consistent with simulation experiments. We demonstrate the effectiveness of this approach by analyzing a representative OCDMA scheme with various system parameters. The derived performance metrics have proven effective in characterizing the OCDMA network dynamics.