In this paper, the performance of VoIP on IPv4, IPv6 and 6in4 protocol with and without IPsec is compared. RTT (Round Trip Time), Throughput, Jitter and CPU usage are compared in VoIP networks. The results for throughput are almost same for both operating systems. CPU usage was higher on both operating systems with IPsec enabled and the results for RTT and Jitter were inconsistent. In general, the results indicated that Fedora 16 performance was better than Windows 7. The results show that although IPSec can add security, it can reduce the VoIP performance in terms of higher delay and higher CPU usage.