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Anonymity technologies such as mix networks have gained increasing attention as a way to provide communication privacy. Mix networks were developed for message-based applications such as e-mail, but researchers have adapted mix techniques to low-latency flow-based applications such as anonymous Web browsing. Although a significant effort has been directed at discovering attacks against anonymity networks and developing countermeasures to those attacks, there is little systematic analysis of the quality of service (QoS) for such security and privacy systems. In this paper, we systematically address TCP performance issues of flow-based mix networks. A mix's batching and reordering schemes can dramatically reduce TCP throughput due to out-of-order packet delivery. We developed a theoretical model to analyze such impact and present formulas for approximate TCP throughput in mix networks. To improve TCP performance, we examined the approach of increasing TCP's duplicate threshold parameter and derived formulas for the performance gains. Our proposed approaches will not degrade the system anonymity degree since they do not change the underlying anonymity mechanism. Our data matched our theoretical analysis well. Our developed theoretical model can guide the deployment of batching and reordering schemes in flow-based mix networks and can also be used to investigate a broad range of reordering schemes.