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Internet is a ubiquitous part of businesses and individuals worldwide. With its popularity on an incline, operating system vendors are developing end-systems that support the new version of Internet Protocol (IPv6) that eventually will replace IPv4. The new version resolves issues that IPv4 has and takes the Internet into the 21st century. Performance of the IP stack and how it associates with operating systems is critical to the efficiency of all network related activities on any computing infrastructure. Hence it is essential to evaluate performance of IP stack with different operating systems. In this paper, two Microsoft operating systems namely, Windows XP and Windows Server 2003 are configured with the two versions of IP and empirically evaluated for performance difference. The experimental results demonstrate that theoretical and practical performance values are different. It also shows that network performance depends not only on IP version and traffic type, but also on the choice of the operating system.