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TCP/IP is the suit of protocols that is designed for networks consisting of segments connected with routers. It also provides communication on smaller networks. Internet Protocol (IP) version 4 is the standard for the design and interconnection of networks today; however it has limitations that hinder its growth. The newer version of the protocol, IPv6, addresses issue that inherently are of concern in the older version, and also offers new opportunities that enrich communication experiences of users. But like any new technology, IPv6 has its associated limitations. It has 128bit packet structure and thus there are associated increased overheads. This increased overhead and its impact on host and network operating systems may lead to network performance issues. In this paper, five Windows operating systems are configured with the two versions of IP and empirically evaluated for performance difference. Performance related metrics like throughput, latency and round trip time are measured on a test-bed implementation. The results show that network performance depends not only on IP version and traffic type, but also on the choice of the operating system.