Implementing IPv6 in modern client/server operating systems (OS) will have drawbacks of lower throughput as a result of its larger address space. In this paper we quantify TCP performance for IPv6 on two open source systems (OSs), namely, the Linux based server operating systems - Red Hat Enterprise Server (RHES) and Ubuntu Server. We measure and evaluate the key parameters influencing OS behavior and network performance, including TCP throughput, round trip time (RTT), CPU usage and jitter by observing OS kernel reactions. Our findings reported in this paper provide some insights into IPv6 performance with respect to the impact of modern and commonly used Linux server operating systems. This study may help network researchers and engineers in selecting better OS in the deployment of IPv6 on corporate networks.