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

Director of ECDC is Zsuzsanna Jakab. In her work she is aided by the Executive Management Committee  (EXC). The Directors Cabinet  (DIR) carries out the overall coordinating role, and is responsible for external relations and country cooperation.

The organisational structure of ECDC is based on four technical units. The disease-specific activities are managed in horizontal disease programmes  across the four technical units. These horizontal programmes are the corner stones of the disease-specific scientific output of the Centre.