In this paper we discuss the impact the use of IPv6 has on remote penetration testing of servers and web applications. Several modifications to the penetration testing process are proposed to accommodate IPv6. Among these modifications are ways of performing fragmentation attacks, host discovery and brute-force protection. We also propose new checks for IPv6-specific vulnerabilities, such as bypassing firewalls using extension headers and reaching internal hosts through available transition mechanisms.The changes to the penetration testing process proposed in this paper can be used by security companies to make their penetration testing process applicable to IPv6 targets.