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There are no statistics dealing specifically with the casualties of the Croat-Bosniak conflict along ethnic lines. However, according to The RDC's data on human losses in the regions, in Central Bosnia 62 percent of the 10,448 documented deaths were Bosniaks, while Croats constituted 24 percent and Serbs 13 percent. The municipalities of Gornji Vakuf and Bugojno are geographically located in Central Bosnia (known as Gornje Povrbasje region), but the 1,337 region's documented deaths are included in Vrbas regional statistics. Approximately 70–80 percent of the casualties from Gornje Povrbasje were Bosniaks. In the region of Neretva river, of 6,717 casualties, 54 percent were Bosniaks, 24 percent Serbs and 21 percent Croats. The casualties in those regions were mainly, but not exclusively, the consequence of Croat-Bosniak conflict.

According to the UN, there were 167 fatalities amongst UNPROFOR personnel during the course of the force's mandate, from February 1992 to March 1995. Of those who died, three were military observers, 159 were other military personnel, one was a member of the civilian police, two were international civilian staff and two were local staff.

In a statement in September 2008 to the United Nations General Assembly, Dr Haris Silajdžić, said that "According to the ICRC data, 200,000 people were killed, 12,000 of them children, up to 50,000 women were raped, and 2.2 million were forced to flee their homes. This was a veritable genocide and sociocide". However, Silajdžić and others have been criticised for inflating the number of fatalities to attract international support. An ICRC book published in 2010 cites the total number killed in all of the Balkan Wars in the 1990s as "about 140,000 people".

Many of the 34,700 people who were reported missing during the Bosnian war remain unaccounted for. In 2012 Amnesty reported that the fate of an estimated 10,500 people, most of whom were Bosnian Muslims, remained unknown.ICRC Annual Report 2010 , icrc.org; accessed 25 May 2015, p. 345 Bodies of victims are still being unearthed two decades later. In July 2014 the remains of 284 victims, unearthed from the Tomasica mass grave near the town of Prijedor, were laid to rest in a mass ceremony in the northwestern town of Kozarac, attended by relatives.

The UNCHR stated that the conflict in Bosnia and Herzegovina forced more than 2.2 million people to flee their homes, making it the largest displacement of people in Europe since the end of World War II.