Before the attacks of September 11, 2001, the U.S. federal government had a list of 16 people deemed "no transport" because they "presented a specific known or suspected threat to aviation." The list grew in the immediate aftermath of the September 11 attacks, reaching more than 400 names by November 2001, when responsibility for keeping it was transferred to the Federal Aviation Administration (FAA). In mid-December 2001, two lists were created: the "No Fly List" of 594 people to be denied air transport, and the "Selectee" list of 365 people who were to be more carefully searched at airports. By 2002, the two lists combined contained over a thousand names, and by April 2005 contained about 70,000 names. For the first two and a half years of the program, the Federal Bureau of Investigation (FBI) and Transportation Security Administration (TSA) denied that the program existed.

In 2004, then-U.S. Senator Edward Kennedy was denied boarding a flight because his name was similar to an alias found on the No Fly List. Laura K. Donohue would later write in The Cost of Counterterrorism: Power, Politics, and Liberty that "antiwar activists, such as Jan Adams and Rebecca Gordan, and political opponents of the Bush administration, such as Senator Edward Kennedy and civil rights attorney David Cole, found themselves included." In June 2016, Timothy Healy, the former director of the FBI Terrorist Screening Center, disputed the claim that Kennedy had ever appeared on the list, saying that another person with a similar name—who had accidentally tried to bring ammunition on to a plane—was placed on an airline's watch list and Kennedy was mistakenly detained by the airline, not based on the No Fly List. In October 2006, CBS News' 60 Minutes reported on the program after it obtained a March 2006 copy of the list containing 44,000 names.

Many individuals were "caught in the system" as a result of sharing the exact or similar name of another person on the list; TSA officials said that, as of November 2005, 30,000 people in 2005 had complained that their names were matched to a name on the list via the name matching software used by airlines. In January 2006, the FBI and ACLU settled a federal lawsuit, Gordon v. FBI, brought by Gordon and Adams under the Freedom of Information Act in order to obtain information about how names were added to the list. Under the settlement, the government paid $200,000 in the plaintiffs' attorneys' fees. A separate suit was brought as a class action "filed by people caught in the name game." In response, "TSA created an ombudsman process, whereby individuals now can download and print out a Passenger Identity Verification Form and mail it, along with certain notarized documents, to the TSA 'so the agency can differentiate the individual from others who may be on the list.'"

In April 2007, the U.S. federal government's "terrorist watch list" administered by the Terrorist Screening Center (which is managed principally by the FBI) contained 700,000 records. A year later, the ACLU estimated the list to have grown to over 1,000,000 names and to be continually expanding. However, according to Homeland Security secretary Michael Chertoff, in October 2008 the No Fly List contained only 2,500 names, with an additional 16,000 "selectees" who "represent a less specific security threat and receive extra scrutiny, but are allowed to fly."

As of 2011, the list contained about 10,000 names. In 2012, the list more than doubled in size, to about 21,000 names as the list now included people who were a threat to security outside aviation. In August 2013, a leak revealed that more than 47,000 people were on the list. In 2016, California Senator Dianne Feinstein disclosed that 81,000 people were on the No Fly List.

There is a huge, secretive US anti-terrorism database for Canada specifically, "Tuscan" (Tipoff US/Canada), revealed by Canada's access to information system. The database is used by both the US and Canada, and applies to all borders, not just airports. It is believed to contain information on about 680,000 people thought to be linked with terrorism. The list was created in 1997 as a consular aid. It was repurposed and expanded after 9/11, and again in 2016. The names in Tuscan come from the US Terrorist Identities Datamart Environment (Tide), which is vetted by the FBI's Terrorist Screening Center and populates various US traveller databases, Canada's Tuscan and the Australian equivalent, "Tactics".