ISA Server does not handle IPv6 traffic. IPv6 traffic will pass through the ISA Server firewall regardless of your firewall policy. We recommend that you not enable IPv6 traffic on the ISA Server computer or array. If you have enabled IPv6 traffic, we recommend that you disable it on the ISA Server computer, or on each member of the ISA Server array.
To disable the IPv6 stack, on the ISA Server computer or array member, type the following at a command prompt:
netsh interface ipv6 uninstall
Alternatively, you can disable the IPv6 stack in the Windows user interface:
Note: You only have to perform this procedure on one network connection on the ISA Server computer (Standard Edition) or on one network connection on each ISA Server array member (Enterprise Edition).
Nathan BigmanISA Server User Education
The question on mailing lists is usually if a PC on the network has v.6 installed and ISA does not, does ISA pass the traffic through or prevent it?
But ISA RTM will work if ipv6?
If a PC on the network has v.6 installed, and ISA has it disabled, the traffic will not pass through ISA.
ISA Server 2006 will not handle IPv6 in the RTM version, so the advice provided applies to that version, as well as previous versions of ISA Server.
ISA Server User Education
PingBack from http://www.keyongtech.com/1228055-ip-v6-for-isa-server
The PC on the network may build a IPv6 tunnel such as a 6-to-4 to the anycast address 126.96.36.199 and the first hop for that PC would be the IPv6 address of that anycast server. This is exactly same concept as a VPN tunnel.