Assuming that you are in OS 9, boot up with the OS CD, then find the Disk First Aide in the Utilities folder. Run that. Let it repair the hard drive. You can also use Drive Set up. Do Not hit the initialize button. Just go to the functions menu and select test disk. This will scan your drive and let you know what the problem is. If all goes smooth, you should be able to do a clean install of the OS. Make sure you select that or you will have even more problems.
If you have Norton Utilities, you can boot from that CD and have the Disk Doctor fix any problem it finds also.