Stanisic, 50, left Belgrade on a government plane accompanied by Darko Matijasevic, interior minister for Republika Srpska, the Serbian part of the new Bosnian federation, and Zoran Loncar, a member of the Serbia-Montenegro council for cooperation with the war crimes court in The Hague.
Stanisic had been detained following his surrender, the court said.
The International Criminal Tribunal for former Yugoslavia said Stanisic would face 10 indictments for crimes against humanity and war crimes allegedly committed when he was interior minister – during the opening phases of the 1992-95 Bosnian war, which cost some 200,000 lives.
The indictment said he was responsible for moves to "permanently remove and ethnically cleanse, by force or other means, Bosnian Muslims, Bosnian Croats and other non-Serbs from the territory of the planned Serbian state".
In an interview with the Bosnian-Serb SRNA news agency, Stanisic said he was innocent of the charges and was looking forward to his day in court.