From NCBI:

NCBI now supports IPv6 (beta) for data downloads at http://bit.ly/xiQAsj. More information at  http://1.usa.gov/x655AL .

Please note that NCBI will be taking part in the World IPv6 Launch (http://www.worldipv6launch.org/). On that day (currently anticipated as June 6, 2012), we plan to add IPv6 service to our main FTP Server (http://bit.ly/yerWAX) and shortly thereafter sunset the use of this FTP6 test address (http://bit.ly/xiQAsj).