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In this paper the comparative analysis of the two versions of Internet Protocol viz. IPv4 and IPv6 is presented based on throughput as the network performance metric. The throughput is measured for the application layer Domain Name System (DNS) traffic over the transport layer protocols. The throughput measurements are repeated for Voice traffic with different voice samples and computer gaming traffic characteristics. The experiments are performed on two machines connected via crossover cable in Windows 2007 and Windows 2008 client server environment. The measurements are facilitated by the simulated DNS and software coded voice samples present in the latest version of D-ITG 2.8.0rcl tool. The results show that network performance varies not only with Internet protocol (IP) version but also with the transport layer protocols and the voice samples. The maximum throughput difference observed for G711.2 Voice sample is 86.09 percent.