The Special Department for War Crimes was established after a set of laws had been adopted by the BiH Parliament in December 2004 which were necessary to prosecute cases before the national judicial institutions and to take over the role of the ICTY Rules of the Road Unit which had been reviewing war crime cases before its closure. The Special Department for War Crimes is responsible for prosecution of war crime cases committed in the territory of Bosnia and Herzegovina during the armed conflict from 1992 until 1995.
Department for War Crimes of the Prosecutor’s Office of BiH commenced its work on 9 March 2005. Many officials of the BiH Judiciary, the Hague Court and the International Community were present at the inauguration.
Within the activities of the Special Department for War Crimes, the Collegium of Prosecutors passed the Book of Rules on the Review of War Crime Cases which comprise a document called Orientation Criteria for Assessment of Sensitivity of the Rules of the Road Cases. The purpose of this document is to provide guidelines on selection of cases to be prosecuted by the Prosecutor’s Office of BiH and those that can be referred for further prosecution to the Prosecutor’s Offices with subject-matter and territorial jurisdiction. Due to a large number of war crime cases it may be expected that most of them will be prosecuted at the cantonal/district level.

The Special Department for War Crimes of the Prosecutor’s Office of BiH works on four categories of cases:

• Cases referred by the ICTY to the national judiciary pursuant to Rule 11bis of its Rules of Procedure and Evidence. Those are the cases in which the ICTY confirmed the Indictment but the main trial has not started yet, and the Referral Bench has rendered a final decision to refer a case to the national judiciary for further prosecution. Rule 11bis, inter alia, stipulates the following under Article A:
  (A) After an indictment has been confirmed and prior to the commencement of trial, irrespective of whether or not the accused is in the custody of the Tribunal, the President may appoint a bench of three Permanent Judges selected from the Trial Chambers (hereinafter referred to as the “Referral Bench”), which solely and exclusively shall determine whether the case should be referred to the authorities of a State:
  (i) in whose territory the crime was committed; or
  (ii) in which the accused was arrested; or
  (iii) having jurisdiction and being willing and adequately prepared to accept such a case,
  so that those authorities should forthwith refer the case to the appropriate court for trial within that State.
• Cases previously reviewed by the Rules of the Road Unit. Those are the cases in which the national institutions had conducted investigation and the forwarded them to the Rules of the Road Unit for their review in order to assess if there was sufficient evidence for grounded suspicion that a person could be held in custody.
• Cases from the ICTY OTP in which the Tribunal conducted investigation but has not filed Indictments.
• All the new cases initiated before the closure of the Rules of the Road Unit in October 2004.

The Special Department for War Crimes must also review all the other cases of the Prosecutor’s Offices of Bosnia and Herzegovina which were not submitted to the Rules of the Road Unit in order to assess them as “highly sensitive” (implying that a case is to be prosecuted before the Court of BiH) or “sensitive” (implying that it may be referred to the Prosecutor’s Office with subject-matter and territorial jurisdiction for further proceedings) in line with the Book of Rules and the Orientation Criteria.

As of January 1, 2010 War Crimes Department employs 14 National and 1 International Prosecutors thus it is the largest department of the Prosecutor's Office of BiH with the highest number of Prosecutors. Pursuant to the Decision of the High representative extending the mandate to International Prosecutors the HJPC is expected to appoint additional International Prosecutors to the Special Department for War Crimes. A large number of international and national legal associates, case managers, administrative and other professional personnel are working for this War Crimes Department.  The Department is divided into teams which cover certain geographical regions. Each team is headed a National Prosecutor:

Team 1 covers the region of Northwest Bosnia and a part of Posavina;
Team 2 covers the region of Central Bosnia;
Team 3 covers the region of Eastern Bosnia (the Drina Valley) and a part of Posavina;
Team 4 covers the region of Sarajevo and Eastern Bosnia including Foča;
Team 5 covers the region of Western Herzegovina and the Neretva Valley; and
Special Team 6 for the area of Srebrenica.

Organizational chart of The Department for War Crime