Presuming you are using Lion or Mountain Lion.....Try performing a "Repair Disk" and a "Repair Disk Permissions" from Disk Utility within your Recovery Partition. Boot to the Recovery Partition by holding down the OPTION key, while booting and then selecting the Recovery Partition as the boot device. Then use Disk Utility to perform the disk repairs.
If those two option fail to repair the disk, you probably want to reinstall the operating system from the Recovery Partition. Doing so, without disk erasure, will simply do what is called a "repair installation", and will not disturb your data, settings, or applications. Failing this, you would use your backup (also presuming you did so).