Institutes are academic facilities concerned with research and student education; they produce publications and host congresses. MHB institutes are internal institutions, i.e. they form part of the university in terms of organization, finances and administration.

In contrast to internal institutes, so called affiliated institutes are legally independent entities in the form of limited liability companies or registered associations. They may have close connections to the MHB via cooperation agreements on the shared use of organisation, staff and facilities but do not form part of the MHB. Two institutes are currently affiliated to the MHB: the Brandenburg Institute of Ultrasound (Brandenburgisches Institut für Ultraschall / BIKUS – website under construction) and the Institute of Rehabilitation Research and Personal Injury Management (Institut für Rehabilitationsforschung und Personenschaden-Management (IRP)).