After the Central Intelligence Agency lost its role as the coordinator of the entire United States Intelligence Community (IC), special coordinating structures were created by each president to fit his administrative style and the perceived level of threat from terrorists during his term.

The US has a different counter-terrorist structure than many of its close allies such as Australia, Canada, France, and the United Kingdom. Each has a structure that fits its particular legal system and culture. A contentious issue is whether there needs to be a domestic intelligence service separate from the FBI, which has had difficulty in breaking away from its law enforcement roots and cooperating with other intelligence services.

The National Counterterrorism Center (NCTC) is no longer in the CIA proper, but is in the Office of the Director of National Intelligence (ODNI). The NCTC, however, contains personnel from the CIA, FBI, Department of Justice, and from other members of the IC. A counterterrorism center did exist in the CIA before the NCTC was established.

Given the restrictions of the National Security Act of 1947, which created the CIA but strictly forbade it from having any domestic police authority, the role of the CIA still has multiple dimensions. The Directorate of Operations (DO) of the CIA can infiltrate or otherwise gain human intelligence (HUMINT) from terrorist organizations, their supporters, or from friendly foreign intelligence services. The NCS has a covert operations capability that, possibly in combination with military units from the United States Special Operations Command (USSOCOM), may take direct military action against terrorist groups outside the United States.

The key CIA counter-terror partner is the FBI, which has the domestic operational responsibility for counter-terrorism, which includes both domestic intelligence collection and domestic police work. In the highly decentralized police system of the United States, the FBI also provides liaison and operates cooperatively with state and local police agencies, as well as with relevant federal units, e.g., the United States Coast Guard, which has an important role in preventing terrorist infiltration by sea. Military units have a specialized Counterintelligence Force Protection Source Operations capability to protect their personnel and operations.

Intelligence Community view of terrorism

The United States Intelligence Community had dealt with terrorism long before the September 11, 2001 attacks, including support of guerrillas against the Soviets in Southeast Asia, and other places where the guerrillas' methods may have included terror. In Asia, Latin America, and Africa, the US worked with various foreign governments to suppress terrorism. While government research suggests personality traits that may be common to a substantial number of terrorists, terrorism has few other constants. It has taken place on every continent except Antarctica.

In all these cases, intelligence support from the CIA was required. In some of them, clandestine intelligence collection and covert action by CIA personnel, or those they sponsored, dealt with terrorists and performed counter-terrorist roles.

Many studies of the analysis of, and countermeasures to, terrorism remain classified. Declassified CIA documents on terrorism date back to the late 1970s. According to a 1979 report Western Europe often had opposing terrorist groups in the same conflict at that time, such as nationalists and separatists in Northern Ireland, Spanish nationalists and Basque separatists in Spain and others like them in Turkey. Transnational terrorism was still unusual, although the report noted that the Basque group ETA was active in France as well as Spain.

There are relevant observations from government reports by researchers who have various levels of access into the IC, including the Federal Research Division (FRD) and Congressional Research Service of the Library of Congress. A 1999 FRD study examined some changes from terrorists of the past, especially the emergence of terrorist acts carried out by individuals and members of small, ad hoc groups largely unknown to security organizations. Tactics, as well as sources, had changed, with the greater use of suicide attacks and attacks by women and children.

A very significant concern has been the possible use by terrorists of weapons of mass destruction (WMD).

Weapons of mass destruction Terrorists have already made multiple attacks using WMD, such as chemical attacks by Aum Shinrikyo. A 1996 CIA presentation reviewed the history to date, including Iraq's (now defunct) programs.

Researchers for a 1999 General Accounting Office study had classified access, and concluded that terrorists could use some chemicals like chlorine with relative ease for an attack, while other agents, chemical and biological, would require greater sophistication.

Collection approach HUMINT Efforts to use HUMINT operations with non-official cover, especially in the areas outside the groups' staging areas, have been disappointing. Stepped-up efforts to use non-official cover, especially in Europe, began by creating covers in investment banks and consulting firms. Only several years later was it realized that terrorists would have little to do with such organizations. Another realization was that, even with excellent cover, HUMINT successes would be unlikely to recruit people deep inside the terrorist cells.

Where HUMINT had more potential, and where the cover organizations needed to change to help find appropriate targets, was on the fringes of the terrorist organizations, either groups from which the group would need goods or services, or from people with awareness of the groups but not supporting them. For example, there are reports that 15 cargo ships are linked to al-Qaeda, whose activities at port might draw the attention of security officials, or even low-level dockworkers or craftsmen.

SIGINT Signals intelligence, or SIGINT, is a common tool in espionage, although it has been hard to apply to anti-terrorism activities. The National Security Agency (NSA), the organization formally responsible for SIGINT within the United States intelligence community, was used to targeting conventional military communications systems, while terrorists lacked dedicated communications systems, confronting the NSA with the prospect of "picking out the needles of terrorist transmissions in the haystack". While some information has been gained, SIGINT is only effective against cells if the group is unaware they are being monitored. Once known communication methods have been compromised, terrorists switch to other means. Terrorists may employ various countersurveillance techniques, including the use of non-electronic messengers to avoid interception, employ encrypted message systems, or exploit public Internet connections such as Internet cafes.

The actual interception of messages is probably not done by the CIA, but by NSA or possibly Service Cryptologic Elements (SCE): tactical SIGINT detachments attached to military tactical units. Important communications intercepts have been achieved, with the results clearly available to the CIA. There are cases, however, where a joint CIA-NSA organization places clandestine intercept equipment. The National Security Archive commented, "In 1987, Deputy Director for Science and Technology Evan Hineman established ... a new Office for Special Projects. Concerned not with satellites, but with emplaced sensors – sensors that could be placed in a fixed location to collect signals intelligence or measurement and signature intelligence (MASINT) about a specific target. Such sensors had been used to monitor Chinese missile tests, Soviet laser activity, military movements, and foreign nuclear programs. The office was established to bring together scientists from the DS&T's Office of SIGINT Operations, who designed such systems, with operators from the Directorate of Operations, who were responsible for transporting the devices to their clandestine locations and installing them."

While communications intercepts are usually highly classified, they have come up in US Congressional testimony on terrorism. For example, an FBI official testified with regard to the 1998 United States embassy bombings in Kenya and Tanzania, which took place so closely in time that the terrorist teams can reasonably be assumed to have coordinated their operations in near real-time.

There was independent proof of the involvement of Bin Laden, Al-Qaeda and EIJ Egyptian Islamic Jihad in the bombings. First, the would-be suicide bomber, al-Owhali, ran away from the bomb truck at the last minute and survived. However, he had no money or passport or plan by which to escape Kenya. Days later, he called a telephone number in Yemen and thus arranged to have money transferred to him in Kenya. That same telephone number in Yemen was contacted by Osama Bin Laden's satellite phone on the same days that al-Owhali was arranging to get money.

They have also been revealed in legal proceedings against terrorists, such as United States v. Osama bin Laden et al., indictment, Nov. 4, 1998, and updates.

IMINT The sort of imagery intelligence (IMINT), often from satellites, used against nation-states is of limited use in tracking the movement of groups of small size and little physical infrastructure. More success has come from unmanned aerial vehicles (UAV), which are hard to see and hear, to do such things as follow cars, or loiter above a building, photographic traffic in and out, often with low-light or infrared sensors that work in apparent darkness. For instance, the CIA experimented with the MQ-1 Predator, a small remote-controlled reconnaissance aircraft, to try to spot Bin Laden in Afghanistan, producing probable sightings of the al-Qaeda leader after a series of flights in autumn 2000, overseen by CTC officials and flown by USAF drone pilots at the CIA's Langley headquarters.

FININT Financial intelligence – "following the money" – often can trace the organization behind a particular attack. Once that organization is identified, value transfers from it can point to other operational cells. The term value includes cash and negotiable documents, but also materials such as gems, opium and drugs, and precious metals. The Treasury Department's Office of Foreign Assets Control (OFAC) has the power to "freeze" the accounts of organizations suspected of funding terrorist activities.

Terrorist groups use three types of financing, which are increasingly difficult to track by U.S. intelligence, including the CIA:

Charities, which use both conventional financial institutions and informal value transfer systems, Informal value transfer systems such as hawala and hundi "Commodities- or trade-based money laundering includes the smuggling of bulk cash and the evasion of federal reporting requirements used to track money laundering with commodities such as diamonds, precious metals, gold, and tobacco." The CIA is most likely to gain awareness of commodities and trade transfers outside the United States.

According to the Center for Defense Information (CDI), intelligence agencies help OFAC build its "freeze list" by sending it lists of individuals and organizations believed to be associated with terror, but not all such suspects go onto the freeze list, since the intelligence community can use financial transactions as a means of tracking them.