• Račak massacre (or "Operation Račak") on 15 January 1999 – 45 Albanians were rounded up and killed by Serbian special forces. The first forensic report, by a joint Yugoslavian and Belarusian team, concluded that those killed were not civilians. The massacre provoked a shift in Western policy towards the war.^{[48][49][50][51]}
• Imeraj massacre on 26 March 1999 – Serbian forces entered the village of Pemishtë/Cërkolez and killed 19 Albanian civilians including 13 women and children.^[52]
• Mala Kaludra massacre on 19 April 1999 – 23 Albanian refugees were killed by Serbian paramilitaries as they fled towards Montenegro.^[53]
• Suva Reka massacre on 26 March 1999 – 48 Albanian civilians killed, among them many children.^[54]
• Podujevo massacre – 19 Albanian civilians were killed, including women, children and the elderly.^[55]
• Massacre at Velika Kruša – According to the ICTY, Serbian Special Anti-Terrorist Units murdered 42 persons.^[56] There were also allegations of mass rape.^[57]
• Izbica massacre – Serbian forces killed about 93 Albanian civilians.^[58][59]
• Drenica massacre – there were 29 identified corpses discovered in a mass-grave, committed by Serbian law enforcement.^[60]
• Gornje Obrinje massacre – 18 corpses were found,^[61] but more people were slaughtered.^[62]
• Ćuška massacre – 41 known victims.^[63]
• Bela Crkva massacre – 62 known fatalities^[64]
• Meja massacre – at least 300 persons were killed by Serbian police and paramilitary forces in May 1999.^[65]
• Orahovac massacre – Estimates range from 50 to more than 200 ethnic Albanians killed^[66]
• Dubrava Prison massacre – Prison guards killed more than 70 Albanian prisoners in Dubrava Prison.^[67]
• Poklek massacre – 17 April 1999 – at least 47 people were forced into one room and systematically gunned down. The precise number of dead is unknown, although it is certain that 23 children under the age of fifteen were killed in the massacre.^[68]
• Vučitrn massacre – More than 100 Kosovo refugees were killed by Serbian Police.^[69]

Soon after NATO started bombing Yugoslavia, Slobodan Milošević ordered that all bodies in Kosovo that could be of interest to The Hague Tribunal should be removed.^[70] The Yugoslav Army systematically transported the corpses of Albanians to places like the Trepča Minesnear Kosovska Mitrovica, where their remains were allegedly cremated.^[19]