Just to make sure, you should repair your disk.
Boot to your restore/installer DVD by restarting with the disk in your drive, while holding the letter C.
When you get to the first installer screen (after choosing a language), go to your menus, and choose Disk Utility. It's in your Utilities menu (or the Installer menu if your OS X is older than 10.4). Select your hard drive, and click the Repair Disk button. When that completes, quit Disk Utility, and choose quit again to restart.
If Disk Utility can't repair your problem, then you want to consider replacing the hard drive (after a good backup if you need to do that). Other utilities, such as Disk Warrior are also a good possibility for repair of your present drive.