This research monograph is about transitional justice mechanisms as applied in Bosnia and Herzegovina with a clear focus on criminal justice mechanisms, primarily on national war crimes trials. Bosnia and Herzegovina has been a complex field of experiments for the outreach and referral programm of the International Criminal Tribunal for the former Yugoslavia (ICTY). Meanwhile, most of the war crimes trials that were referred from the ICTY to the domestic jurisdiction have been completed. While these trials were mainly focused on the “big fishes” that were regarded as the most responsible for the atrocities during the 1992–1995 armed conflict, the rest of the suspected war criminals are prosecuted by the national authorities. This study provides an overview of national war crimes prosecutions in Bosnia and Herzegovina focusing on key problems of substantive and procedural criminal law aspects, such as the application of various different Criminal Codes for the same crimes at the state and entity level as well as the introduction and application of plea bargaining in war crimes cases.