​Steno Diabetes Center Copenhagen is headed by Allan Flyvbjerg and is organized in four central units: Clinic (Patient Care), Clinical Research, Education and Health Promotion. In addition, there are three support functions: Staff, CoreLab and Research and Innovation (RIO).

The management of the center consists of the CEO and the managers of the four units: head of clinic Tina Vilsbøll and head nurse of the Clinic Kirsten Engelhard Nielsen,  head of clinical research Birgitte Brock, head of education Ulla Bjerre-Christensen, the position as head of health promotion is vacant and head of administration Charlotte Hove Andreasen.

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