MERCOSUR makes its decisions through three bodies: the Council of the Common Market (CMC), the main body of MERCOSUR which conducts the integration process politically; the Common Market Group (GMC), which oversees the daily functioning of the Bloc; and the Mercosur Trade Commission (CCM), responsible for the administration of common commercial policy instruments. More than 300 negotiation forums assist these bodies in the most diverse areas, integrated by representatives of each States Parties in order to promote initiatives to be considered by decision-making bodies.

Over time and for the purpose of the implementation of its regional policies, MERCOSUR has created several permanent agencies in different cities. Examples of these are the Fund for the Structural Convergence of MERCOSUR (FOCEM), the Institute of Public Policies on Human Rights (IPPDH), MERCOSUR Social Institute (ISM), the Parliament of MERCOSUR (PARLASUR), the Secretariat of MERCOSUR (SM) and the Permanent Review Tribunal (TPR).