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Researches on mobile ad hoc networks have been concentrated on implementations and performance comparisons of routing protocols. Little attention was paid to the interaction between end-to-end TCP traffic flows and these routing protocols. In this paper, we study the performance of two reactive on-demand routing protocols-DSR and AODV based on TCP traffic flows. Our performance simulations show that DSR performs better in a small window size and AODV works better in a large window size. Both of them need further improvements to provide better performance for TCP flow transmission. In addition, current TCP implementations can not guarantee a stable performance because they lack the ability to distinguish packet losses caused by network congestion or by route failure. The effects of interactions among routing, MAC and TCP protocol are also briefly discussed. This paper provides performance comparisons based on several important performance metrics.