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

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.