The Counter Terrorist Unit (also referred to as the Counter Terrorism Unit or CTU) was an intelligence and law enforcement agency in the United States of America which worked to investigate and prevent terrorist acts within U.S. borders.

After Day 6, CTU was disbanded following the supposed extralegal activities of several agents and was under investigation for human rights violations. Its functions were then delegated to other agencies, and the personnel had their government clearance revoked. However, following Day 7, CTU was resurrected with the help of Rob Weiss, who convinced President Taylor to reestablish the agency in full capacity.

The Counter Terrorist Unit was the Department of Homeland Security's intelligence arm, under the National Protection and programmes directorate. The agency was also overseen by the Secretary of Defense. CTU was established after the first bombing of the World Trade centre in 1993.

CTU was headquartered in Washington, DC, and established domestic counter-terrorism divisional field offices in major U.S. metropolitan areas. CTU was to investigate the activities of domestic or foreign terrorists inside America's borders. CTU operations were overseen by both Congress and the Executive Branch of the federal government.

A trial was launched into the past activities of CTU in tracking down and torturing suspects, preventing attacks, and in their methods of practise and activity. CTU was disbanded and all its personnel had their government status revoked. Some were offered jobs at other agencies, but most were left jobless.