In this thesis, we propose a new protocol named Layered TCP with RTT Compensation (LTCP-RC, for short). LTCP-RC is a simple modification to the congestion window response of the high-speed protocol, Layered TCP (LTCP). In networks characterized by large link delays and high RTTs, LTCP-RC makes the LTCP protocol more scalable. Ack-clocked schemes, similar to TCP, suffer performance problems like long convergence time and throughput degradation, when RTT experienced by the flow increases. Also, when flows with different RTTs compete, the problem of unfairness among competing flows becomes worse in the case of high-speed protocols. LTCP-RC uses an RTT Compensation technique in order to solve these problems. This thesis presents a general framework to decide the function for RTT Compensation factor and two particular design choices are analyzed in detail. The first algorithm uses a fixed function based on the minimum RTT observed by the flow. The second algorithm uses an adaptive scheme which regulates itself according to the dynamic network conditions. Evaluation of the performance of these schemes is done using analysis and ns-2 simulations. LTCP-RC exhibits significant performance improvement in terms of reduced convergence time, low drop rates, increased utilization in presence of links with channel errors and good fairness properties between the flows,. The scheme is simple to understand, easy to implement on the TCP/IP stack and does not require any additional support from the network resources. The choice of parameters can be influenced to tune the RTT unfairness of the scheme, which is not possible in TCP or other high-speed protocols. The flexible nature of the analysis framework has laid the ground work for the development of new schemes, which can improve the performance of the window based protocols in high delay and heterogeneous networks.