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Over the last decade, many fundamental changes have occurred in data communications and network infrastructure that will be shaping the future of information technology for years to come. This global network infrastructure, the Internet, is now at the core of communications for worldwide economy and individuals. Internet protocol (IP) v4 is the standard for the design and interconnection of networks today; however it has limitations that hinder its growth. IPv6 is the solution and it has two-fold advantage - it addresses inherent problems in the earlier version protocol, and it offers new opportunities that can enhance communication experiences of users beyond current scope. However, due to the increased overhead in IPv6 and its interaction with the operating system that hosts this communication protocol, there may be network performance issues. In this paper, six operating systems namely, Windows and Linux distributions are configured with the two versions of IP and empirically evaluated for performance difference. Performance related metrics like throughput, delay, jitter and CPU usage 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.