| CAP | combat air patrol | |
| CAPPS | Computer Assisted Passenger Prescreening System | |
| CENTCOM | Central Command | |
| CIA | Central Intelligence Agency | |
| CONR | Continental U.S. NORAD Region | |
| CSG | Counterterrorism Security Group | |
| CTC | Counterterrorist Center | |
| DIA | Defense Intelligence Agency | |
| DCI | Director of Central Intelligence | |
| ESU | Emergency Service Unit (NYPD) | |
| FAA | Federal Aviation Administration | |
| FBI | Federal Bureau of Investigation | |
| FDNY | Fire Department of New York | |
| FFTC | Florida Flight Training Center | |
| FISA | Foreign Intelligence Surveillance Act | |
| FISC | Foreign Intelligence Surveillance Court | |
| INS | Immigration and Naturalization Service | |
| ISID | Inter-Services Intelligence Directorate (Pakistan) | |
| JCS | Joint Chiefs of Staff | |
| JI | Jemaah Islamiah | |
| JTTF | Joint Terrorism Task Force | |
| KSM | Khalid Sheikh Mohammed | |
| Legat | legal attaché | |
| MAK | Mektab al Khidmat | |
| MON | memorandum of notification | |
| NEADS | Northeast Air Defense Sector | |
| NCTC | National Counterterrorism Center | |
| NGO | nongovernmental organization | |
| NMCC | National Military Command Center | |
| NORAD | North American Aerospace Defense Command | |
| NTSB | National Transportation Safety Board | |
| NSA | National Security Agency | |
| NSC | National Security Council | |
| NSPD | national security policy directive | |
| NYPD | New York Police Department | |
| OEM | Office of Emergency Management (New York City) | |
| OFAC | Office of Foreign Assets Control | |
| OIPR | Office of Intelligence Policy and Review | |
| OMB | Office of Management and Budget | |
| PAPD | Port Authority Police Department | |
| PDD | presidential decision directive | |
| PEOC | Presidential Emergency Operations Center | |
| SEC | Securities and Exchange Commission | |
| TSA | Transportation Security Administration | |
| TTIC | Terrorist Threat Integration Center | |
| UBL | Usama Bin Ladin | |
| WMD | weapons of mass destruction | |
| WTC | World Trade Center | |
| WTO | World Trade Organization |