From the Sept. 9, 2013 Congressional Research Service Report: Security Clearance Process: Answers to Frequently Asked Questions.
A security clearance is a determination that an individual—whether a direct federal employee or a private contractor performing work for the government—is eligible for access to classified national security information. A security clearance alone does not grant an individual access to classified materials. Rather, a security clearance means that an individual is eligible for access. In order to gain access to specific classified materials, an individual should also have a demonstrated “need to know” the information contained in the specific classified materials.
There are three levels of security clearances: Confidential, Secret, and Top Secret, which correspond to the levels of sensitivity of the information that a cleared individual will be eligible to access. In addition, there are two major categories of classified information that are commonly associated with the Top Secret level: Sensitive Compartmented Information (SCI), which refers to intelligence sources and methods, and Special Access Programs (SAPs), which refers to highly sensitive policies, projects, and programs. These categories exist for classified information that has been deemed particularly vulnerable. Eligibility standards and investigative requirements for access to SCI and SAPs are higher than for access to information otherwise classified at the same level, which further restricts the number of individuals eligible for access.