Run CHKDSK in readonly mode. This will tell you what is wrong with the file system.
Then try a comprehensive SMART diagnostic. Look for reallocated, pending, or uncorrectable sectors. This will tell you if the drive has physical problems.
HD Sentinel (DOS / Windows / Linux): http://www.hdsentinel.com/
HDDScan for Windows: http://hddscan.com/
See this article for SMART info: http://en.wikipedia.org/wiki/S.M.A.R.T.
Your next step will depend on what you find.