Stanišić was prosecuted for war crimes in Croatia and Bosnia and Herzegovina in the period from 1991 to 1995, before the International Criminal Tribunal for the former Yugoslavia (ICTY) together with Franko Simatović. He was initially acquitted on 30 May 2013 by the ICTY for his role in the wars but the verdict was later overturned on 15 December 2015 after successful appeal by the prosecutors (ICTY Appeals Chamber). The retrial before the UN Mechanism for International Criminal Tribunals (MICT) has commenced on 13 June 2017. The base of Stanišić and Simatović's operations was revealed to be in western Bosnia, where they commanded regional forces. On 30 June 2021, he was found guilty under counts of murder, deportation, forcible transfer and persecution as crimes against humanity that occurred during the Bosanski Šamac ethnic cleansing, and sentenced to 12 years in prison.
