A small network of computing devices that started as ARPANET project in early 1980s is now a worldwide network of devices for billions of users. This global network, the Internet, has become an integral part of worldwide economy and life of individuals. Internet Protocol (IP) v4 is the basic building block of the Internet and has served well, but it has limitations that hinder its growth. The solution is IPv6, which addresses inherent problems of the earlier version. 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, two operating systems namely, Windows Vista and Linux Ubuntu 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 empirically 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.