Howtoforge posted a tutorial about how you can run your own DNS servers (primary and secondary) with ISPConfig 3.

To do this, you need two servers with two different public IP addresses and with ISPConfig 3 installed. I will use Debian Squeeze for both DNS servers here to demonstrate the base system setup process and ISPConfig 3 installation, but once you have ISPConfig 3 installed on your servers, the configuration inside ISPConfig 3 is identical, no matter what distribution you use.

  How To Run Your Own DNS Servers (Primary And Secondary) With ISPConfig 3 (Debian Squeeze)