Disk Utility, which can be found in the Applications > Utilities folder is a useful program for repairing the Disk and Disk Permissions, but it can’t do repairs to the Partition (usually called Macintosh HD). The option to Repair Disk is greyed out. This is because it can’t do repairs to the same partition it is running from.
In order to effect repairs to the Partition the Mac needs to be restarted in Single User Mode. The repair program called File System Consistency Check or fsck is built in to Mac OS X, which can be accessed from the command line
OS X – Single User Mode
To verify or repair your Mac with fsck, restart your Mac and as soon as you hear the startup tone hold down the Command (cmd) and S keys on the keyboard. Continue to hold down those keys until a black screen with white lettering appears. (Depending on your OS version and preferences it might first ask you for the password).
As the Mac boots up in this Single User Mode the screen will scroll down until eventually stops. The last line should end in
At the root# prompt type the following:
then press the Return key
Each part of the Hard Drive will then be checked, and after a few minutes it will report the status of the drive and if was repaired or modified.
The root# prompt will also then reappear on the last line.
This time at the prompt type:
and press the Return key
Your Mac should then continue to start up normally