| Affiliate/Subgroup | Scope | Center of Gravity | |
 9-11 plotters | International | Afghanistan | |
| 9-11 Second Wave Plotters |  National | Pakistan | |
| Abu Sayyaf | National | Philippines | Active |
| Al-Gamaa al-Islamiyya | International | Egypt | |
| Al-Ghuraba | Local | Pakistan | |
| Al-Qaeda Fatwah Committee | International | Afghanistan | |
| Al-Qaeda Finance Committee |  International | Pakistan | |
| Al-Qaeda in Iraq | Regional | Iraq | Active |
| Al-Qaeda majlis al shura | International | Afghanistan | |
| Al-Qaeda Media Committee | International | Pakistan | |
| Al-Qaeda Military Committee | International | Afghanistan | |
| Al-Qaeda Travel Subcommittee | International | | |
| Al Hijra | Local | Sudan | |
| al Themar al Mubaraka | Local | Khartoum, Sudan | |
| Al Wafa | International | Saudi Arabia | |
| American Airlines Flight 11 Hijackers | Local | Boston, Massachusetts, United States | |
| American Airlines Flight 77 Hijackers | Local | Washington, DC, United States | |
| Ansar al-Sunna | National | Iraq | Active |
| As-Sahab | International | Pakistan | Active |
| Asma Limited | Local | Nairobi, Kenya | |
| Benevolence International Foundation Sarajevo Office | Regional | Sarajevo, Bosnia-Herzegovina | |
| Dar Es Salaam embassy bombing cell | Local | Dar Es Salaam, Tanzania | |
| East Africa Embassy Bombers | Regional | Kenya | |
| East Turkistan Islamic Movement | National | China | Active |
| Egyptian Islamic Jihad | Regional | Egypt | |
| Global Islamic Media Front | International | Pakistan | Active |
| Hamburg Cell | International | Germany | |
| Harakat-ul-Jihad-I-Islami Bangladesh | National | Bangladesh | Active |
| Harakat ul-Jihad-I-Islami | Regional | Kashmir | Active |
| Harakat ul-Mujahedin | Regional | Kashmir | Active |
| Hezba Nahda | National | Tajikistan | |
| International al-Ikhlas Company | International | Khartoum, Sudan | |
| Islamic Army of Aden | National | Yemen | Active |
| Islamic International Peacekeeping Brigade | Regional | Chechnya | Active |
| Islamic Movement of Uzbekistan | Regional | Uzbekistan | Active |
| Islamic State of Iraq | National | Iraq | |
| Jamaat e Jihad Eritrea | National | Eritrea | |
| Jamaat e Jihal al Suri | National | Syria | |
| Jamat Nasiyah Dawa | Local | United Kingdom | |
| Jemaah Islamiya | Regional | Indonesia | Active |
| Jordan Millennium Bombing Cell | Local | Jordan | |
| Khartoum Tannery | Local | Khartoum, Sudan | |
| Lackawanna Six | Local | Lackawanna, New York, United States | |
| Ladin International | Local | Khartoum, Sudan | |
| Libyan Islamic Fighting Group | National | Libya | |
| Mantiqi I | Regional | Malaysia | |
| Moro Islamic Liberation Front | National | Philippines | |
| Mujahideen Shura Council | National | Iraq | Active |
| Nairobi embassy bombing cell | Local | Nairobi, Kenya | |
| Qudarat Transport Company | Local | Khartoum, Sudan | |
| Sajana Tower Fruit and Vegetable Company | Local | Sudan | |
| Salafist Group for Preaching and Combat | Regional | Algeria | Active |
| Spanish al-Qaeda cell | Local | Spain | |
| Taba Investments | Local | Sudan | |
| Talah e Fatah | International | Egypt | |
| Taliban | National | Afghanistan | Active |
| United Airlines Flight 175 Hijackers | Local | Boston, Massachusetts, United States | |
| United Airlines Flight 93 Hijackers | Local | Newark, New Jersey, United States | |
| Wadi al Aqiq | Local | Sudan | |
| Yemen Jannubi Group | National | Yemen | |
| 3-11 Madrid train bombers | Local | Madrid, Spain | |
| Hizb-I Islami Gulbuddin | Local | Afghanistan | Active |
| Islamic Jihad Group of Uzbekistan | International | Uzbekistan | Active |
| Riyadus-Salikhin Reconnaissance and Sabotage Battalion of Chechen Martyrs | Local | | Active |
| 2002 French poison cell | Local | France | |
| 7-7 London transit bombers | Local | London, United Kingdom | |
| Al-Badhr Mujahedin | Local | Pakistan | Active |
| Al-Ittihad al-Islami | National | Somalia | |
| Armed Islamic Group | Regional | Algeria | |
| Asbat al-Ansar | National | Lebanon | Active |
| Jaish-e-Mohammed | Regional | Kashmir | Active |
| Jund al-Sham | National | Syria | Active |
| Lashkar e-Tayyiba | National | Kashmir | Active |
| Mantiqi II | National | Indonesia | Active |
| Moroccan Islamic Combatant Group | Regional | Morocco | Active |
| Project Bojinka Cell | Regional | Philippines | |
| Tehrik-e-Nifaz-e-Shariat | Local | Pakistan | Active |
| Tunisian Combatant Group | Regional | Tunisia | Active |
| UK-US airline bomb plotters | International | United Kingdom | |
