This page (the very bottom of it) might give some ideas (it's for Core 5, I take it that you are using Fedora Core though you didn't mention it, but it could work for you too):
1) check if your conf file exists:
if you get file listed, it's there -- if you don't get, it's missing
2) if the file was missing: check if backup exists:
if it doesn't exist, jump to 3); otherwise try first to (su -- become root, asks for your root password)
cp /etc/yum.conf~ /etc/yum.conf
and after this re-try running the update tool
3) if no backup exists or if the above step didn't work, your file might be corrupt. The link I provided has information about how you deal with this problem: basically you remove the config file and then download a new one (from Fedora).