From 1991 Stojan Župljanin was commander of the Regional Security Services Centre (CSB) of Banja Luka in northern Bosnia and Herzegovina (BiH). From May 1992 until July 1992 he was a member of the Autonomous Region of Krajina (ARK) Crisis Staff, and in 1994 he became advisor for internal affairs to the President of Republika Srpska (RS).
Župljanin was originally indicted in March 1999 by the International Criminal Tribunal for the former Yugoslavia. In September 2008, Župljanin’s indictment was consolidated with the indictment of Mićo Stanišić. Župljanin is charged with 10 counts of crimes against humanity and violations of the laws or customs of war in particular against Muslim and Croatian civilians. These include murders, extermination, deportation, torture and other crimes committed in north western BiH between April and December 1992.
On 10 June 2008, Stojan Župljanin was arrested by the Serbian authorities near Belgrade. He was transferred on 21 June 2008 in to the ICTY's custody. Župljanin has pleaded not guilty to all charges. The trial commenced on 14 September 2009. Župljanin pleaded not guilty to all charges.
The prosecution case began on 14 September 2009 and was completed on 1 February 2011.
The defence case commenced on 11 April 2011.