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The structural units of the institute are its departments and divisions. The institute comprises its Forensic Medical Departments, the Biometrics Department, the DNA Department, the Document Department, the IT-Department, the Chemistry Department, the Toxicology Department, the Vehicle and Road Accident Investigation Department, the Technical Department, the Economic Division, the Administration Division, the Quality Division and the Personnel Division.

Regional forensic medical departments are in Tallinn, Tartu, Kohtla-Järve and Pärnu.

The main functions of structural units in their working areas are set out in the statutes of the institute. More detailed tasks for each unit are set out in the statutes of individual units, as approved by the director.