n June 1991, MladiÄ was promoted to Deputy Commander of the Pristina Corps in Kosovo at a time of high tension between Serbs and Kosovo's majority Albanian population. That year, MladiÄ was given command of the 9th Corps of the Yugoslav People's Army (JNA), and led this formation against Croatian forces in Knin, the capital of the self-declared Republic of Serbian Krajina.[18] On 4 October 1991, he was promoted to Major General. The JNA forces under his command participated in the Croatian War, notably during Operation Coastline 91 in an attempt to sever Dalmatia from the rest of Croatia, which failed even though the JNA forces were much more heavily armed and outnumbered the Croatian forces substantially. Among other things, MladiÄ helped Milan MartiÄ's paramilitary take the village of Kijevo.
On 24 April 1992, MladiÄ was promoted to the rank of Lieutenant Colonel General. On 2 May 1992, one month after the Bosnian Republic's declaration of independence, MladiÄ and his generals blockaded the city of Sarajevo, shutting off all traffic in and out of the city, as well as water and electricity. This began the four-year Siege of Sarajevo, the longest siege in the history of modern warfare. The city was bombarded with shells and random shooting from the guns of snipers. On 9 May 1992, he assumed the post of Chief of Staff/Deputy Commander of the Second Military District Headquarters of the JNA in Sarajevo. The next day, MladiÄ assumed the command of the Second Military District Headquarters of the JNA.
On 12 May 1992, in response to Bosnia's secession from Yugoslavia, the separatist Bosnian Serb Parliament voted to create the VRS, or Army of Republika Srpska. At the same time, MladiÄ was appointed Commander of the Main Staff of the VRS, a position he held until December 1996. (In May 1992, after the withdrawal of JNA forces from Bosnia, the JNA Second Military District became the nucleus of the Main Staff of the VRS.) On 24 June 1994, he was promoted to the rank of Colonel General over the approximately 80,000 troops stationed in the area.
In July 1995, troops commanded by MladiÄ, harried by NATO air strikes intended to force compliance with a UN ultimatum to remove heavy weapons from the Sarajevo area, overran and occupied the UN safe areas of Srebrenica and Žepa. At Srebrenica over 40,000 Bosniaks who had sought safety there were expelled. An estimated 8,300 were murdered, allegedly on MladiÄ's order.[19][20] In November 1995, when Judge Fouad Riad indicted MladiÄ for genocide in Srebrenica at the war crimes tribunal in The Hague, he stated that the events were "Truly scenes from hell, written on the darkest pages of human history".[21]
On 4 August 1995, with a huge Croatian military force poised to attack the Serb-held Krajina region in central Croatia, Radovan KaradžiÄ announced he was removing MladiÄ from his commandant post and assuming personal command of the VRS himself. KaradžiÄ blamed MladiÄ for the loss of two key Serb towns in western Bosnia that had recently fallen to the Croats, and he used the loss of the towns as the excuse to announce his surprise command structure changes.[22] MladiÄ was demoted to an "adviser". He refused to go quietly, claiming the support of both the Bosnian Serb military as well as the people. KaradžiÄ countered by attempting to pull political rank as well as denouncing MladiÄ as a "madman," but MladiÄ's obvious popular support forced KaradžiÄ to rescind his order on 11 August.[23]
On 8 November 1996, the President of the Bosnian Serb Republic, Biljana PlavÅ¡iÄ, dismissed MladiÄ from his post. He continued to receive a pension until November 2005.[24]