A security check is a determination by the United States government that a person or company is eligible for access to classified information. There are two types of checks: Personnel Security Checks (PCL) and Facility Security Check (FCL). Government agencies that issue checks often refer to checks as “eligibility for access.
What are the security check levels?
Security checks can be issued by many United States government agencies, including the Department of Defense (DoD), the Department of Homeland Security, the Department of Energy (DoE), the Department of Justice, and the Central Intelligence Agency. DoE checks include the “L,” and “Q” levels. DoD issues more than 80% of all checks. There are three levels of DoD security checks:

• Confidential
• Secret
• Top Secret.

What types of things can prevent someone from receiving a security check?

• Criminal conviction resulting in incarceration for a period of one year or more
• Current unlawful use of or addiction to a controlled substance
• Determined to be mentally incompetent by a mental heath professional approved by DoD
• Discharge or dismissal from the Armed Forces under dishonorable conditions
• Unwillingness to surrender a foreign passport

Source1:http://www.clearancejobs.com/security_clearance_faq.pdf
Source2:http://answers.ask.com/Computers/Hardware/what_is_a_security_clearance