In 1999, the General Assembly endorsed the recommendations and decisions contained in the Commitment of Mar Del Plata and established CICTE by resolution AG/RES. 1650 (XXIX-O/99) The first regular session of CICTE was held in Miami, Florida, in October 1999 which developed a plan of work.  A second regular session planned for Bolivia in 2000 had to be canceled at the last moment. No session was scheduled in 2001.

The events of September 11, 2001 brought renewed focus to the Inter-American efforts to confront terrorism. The attacks were immediately condemned by the General Assembly, which was meeting in Special Session in Lima, Peru, to approve the Inter-American Democratic Charter.  On September 21, 2001, at the 23rd Meeting of Consultation of Ministers of Foreign Affairs in Washington, D.C., the ministers adopted the  Resolution Strengthening Cooperation to Prevent, Combat, and Eliminate Terrorism (RC.23/RES.1/01) .  Immediately afterwards, the Ministers of Foreign Affairs reconvened in their 24th Meeting of Consultation and approved  the Resolution "Terrorist Threat to the Americas" (RC.24/RES.1/01), declaring that "these terrorist attacks against the United States of America are attacks against all American states" and invoking the the Inter-American Treaty of Reciprocal Assistance (Rio Treaty).

Resolution RC.23/RES.1/01 included among other items the following issues pertinent to CICTE:

• To call upon all member states to strengthen cooperation, at the regional and international levels, to pursue, capture, prosecute, punish and, as appropriate, to expedite the extradition of the perpetrators, organizers, and sponsors of these terrorist acts, strengthen mutual legal assistance, and exchange information in a timely manner.

• To instruct the Permanent Council to convoke, as soon as possible, a meeting of the Inter-American Committee Against Terrorism so that it may identify urgent actions aimed at strengthening Inter-American cooperation to prevent, combat, and eliminate terrorism in the Hemisphere.

• To entrust the Permanent Council with preparing a draft Inter-American Convention Against Terrorism with a view to presenting it to the next session of the OAS General Assembly. Also, to urge the states to study the international legal repercussions of the conduct of government authorities who provide financial support to protect, or harbor terrorist individuals or groups.

In light of these and subsequent resolutions of the organs of the Inter-American system, CICTE held two special sessions October 15, 2001 and November 29, 2001. Between these sessions, three subcommittees (Financial Controls, Border Controls, and Work Plan) worked diligently to identify counter-terrorism actions for OAS Member States to implement at the multi-lateral, regional, sub-regional and national levels and to draft an ambitious although concrete agenda for CICTE to pursue in 2002-2003.

At the Second Regular Session of CICTE January 28-29, 2002 in Washington, DC, the ministers of Interior and Public Security and the other heads of delegations reported on the action taken by their respective nations to implement Resolution RC. 23 of September 21. On January 30, policy experts from the member states participated in a Policy Development Role Playing Exercise hosted by the United States to examine possible courses of action in response to a terrorist scenario.

In 2002, CICTE established an Executive Secretariat within the OAS General Secretariat. The CICTE Secretariat was formed with individuals seconded by the governments of El Salvador, the United States and Uruguay. The OAS Secretary General appointed an Executive Secretary in October 2002 to direct the operations of the secretariat.

A key milestone in 2002 was the drafting and signing of the OAS Convention Against Terrorism. AG/RES. 1840 (XXXII-O/02) Inter-American Convention Against Terrorism This landmark document was signed by 30 of the Organization’s Member States at the OAS General Assembly in Bridgetown, Barbados on June 3, and entered into effect in July 2003. As of November 2006, 22 member states are States Party to the Convention. 

Since 2002, the CICTE Secretariat has developed a full range of technical assistance and capacity building programs to assist OAS Member States to prevent, combat and eliminate terrorism.  Today, there are 10 programs divided into six broad program areas:  border controls, financial controls, critical infrastructure protection, legislative assistance and consultations, crisis management exercises, and policy development and coordination.   The latter program is devoted to promoting international cooperation and coordination with other international, regional, and sub-regional bodies, as well as the private sector.