With the increasing popularity in recent years, many popular Operating System (OS) venders worldwide have incorporated Internet Protocol version6 (IPv6) into their OS. The performance of the IP stack, together with the behavior of the OS greatly affects the efficiency of network applications built on top of it. Like any other protocols, the acceptance of various IPv6 implementations heavily relies on the end-user performance. Hence with the availability of a variety of IPv6 implementations, it is essential to evaluate their performance under different operating systems. An investigation of IPv6 stack performance on three different operating systems namely, Windows2003, Redhat Linux 9.0 (Redhat9.0) and FreeBSD4.9 is discussed in this paper. Performance analysis and comparison of the three IPv6 stacks, some interesting points raised by the experimental results are addressed.