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The Top Secret America database was put together by compiling hundreds of thousands of public records of government organizations and private-sector companies over the past two years.

From these records, The Washington Post identified 45 government organizations (for example, the FBI) engaged in top-secret work and determined that those 45 organizations could be broken down into 1,271 sub-units (for example, the Terrorist Screening Center of the FBI). One of the 45 organizations is represented as “unknown”; this category was created as a catchall for companies doing work for a government organization that could not be determined.

At the private-sector level, The Post identified 1,931 companies engaged in top-secret work for the government. Private-sector companies were grouped together and listed by a parent company's name (for example, General Dynamics), even though one company might contain multiple sub-units (for example, General Dynamics Information Technology).

In a case where a large corporation (for example, Boeing) has a distinctly named sub-unit engaged in top-secret work (for example, Boeing's Digital Receiver Technology), the name of the sub-unit was used. In the case of large corporations not primarily in the defense industry (for example, AT&T) that have similarly named sub-units that focus on top-secret work (for example, AT&T Government Solutions), the name of the parent company is used and the name of the sub-unit is noted. For every company listed, revenue and employee data and the date of establishment were drawn from public filings, Dun & Bradstreet data and original reporting.

State and local government organizations generally do not work at the top-secret level; that type of clearance is rarely granted to state officials. But the organizations are all part of a secretive domestic intelligence and homeland security world. The Post examined nearly 1,000 threat documents marked "For Official Use Only" and collected information from government Web sites, reports and other documents to identify 4,058 government organizations involved in domestic counterterrorism and homeland security. Of the total, 2,880 are federal organizations that work at the state level, such as the FBI's Joint Terrorism Task Forces (JTTFs). There are also 818 state and 360 local organizations. Many of these listed themselves in documents as participants in either Joint Terrorism Task Forces, fusion centers or Anti-Terrorism Advisory Councils in 2009 or 2010.