After the assassination of Zoran Đinđić, Stanišić was arrested on 13 March 2003 during the Operation Sabre by the Serbian Police and handed over to the International Criminal Tribunal for the former Yugoslavia (ICTY) on 11 June 2003. The original indictment against Stanišić and Franko Simatović was created in May 2003, and was later amended several times. He pleaded not guilty to all charges in his first appearance before Court on 13 June 2003. His case was processed together with that of Franko Simatović. He has been charged with persecution, murder, deportation and inhumane acts.