The three bodies of the Centre are the Management Board (MB), the Advisory Forum (AF) and the Director and his staff.

The Director of ECDC is Marc Sprenger. In his work he is aided by the Senior Management Team (SMT). The Director's Office carries out the overall coordinating role, and is responsible for external relations and country cooperation.

The organisational structure of ECDC is based on five units:

• Office of the Chief Scientist 
• Surveillance and Response Support 
• Public Health Capacity and Communication 
• Resource Management and Coordination   
• Information and Communication Technologies

Disease programmes:

• Antimicrobial Resistance and Healthcare-associated Infections
• Emerging and Vector-borne Diseases
• Food- and Waterborne Diseases and Zoonoses
• STI, including HIV and Blood-borne Viruses
• Influenza
• Tuberculosis
• Vaccine-preventable Diseases
• Health Inequalities and Migrant Health