In 2006, Krajišnik was found guilty of committing crimes against humanity during the Bosnian War (1992–95) by the International Criminal Tribunal for the former Yugoslavia (ICTY) and was sentenced to 20 years in prison.

Although Krajišnik had not been indicted by the War Crimes Tribunal – and could therefore participate in Dayton – it was hard to distinguish his views from those of his close friend Radovan Karadžić.

Krajišnik owned a five-hectare farm on the edge of Sarajevo, in an area that would probably revert to the Muslims in any settlement, and we often made bitter jokes that the war was really over Krajišnik's five hectares.Krajišnik was indicted by the ICTY on various charges of crimes against humanity - namely extermination, murder, persecution, deportation, and forced transfer, murder as a war crime, and genocide - in relation to acts committed in 1992 in Bosnia and Herzegovina by Bosnian Serb forces.

[6] On 27 September 2006 Krajišnik was convicted of the following crimes against humanity: extermination, murder, persecution, deportation, and forced transfer.

[1] ICTY judges found that Krajišnik had been part of a joint criminal enterprise which carried out the extermination, murder, persecution and deportation of non-Serbs during the Bosnian war between 1992 and 1995.

[1] Judge Alphons Orie observed that "Krajišnik's role in the commission of the crimes was crucial ... His positions within the Bosnian Serb leadership gave him the authority to facilitate the military, police and paramilitary groups to implement the objective of the joint criminal enterprise".

He noted "Mr Krajišnik... accepted that a heavy price of suffering, death and destruction was necessary to achieve Serb domination.

[citation needed] In 2011, another request for early release was made, according to Krajišnik's brother, Mirko, in response to a British government initiative.

His supporters arrived by bus from across Republika Srpska and convoys of cars were on the streets of Pale with people waving Serbian flags, honking horns, and stopping at the main square as Serb nationalist songs were played.

[12] On 29 August 2020, Krajišnik was taken to the Banja Luka hospital after it was confirmed that he tested positive for COVID-19, amid the COVID-19 pandemic in Bosnia and Herzegovina.