On May 7, 1999, during the NATO bombing of Yugoslavia (Operation Allied Force), five U.S. Joint Direct Attack Munition guided bombs hit the People's Republic of China embassy in the Belgrade district of New Belgrade, killing three Chinese state media journalists and outraging the Chinese public. According to the U.S. government, the intention had been to bomb the nearby Yugoslav Federal Directorate for Supply and Procurement (FDSP). President Bill Clinton apologized for the bombing, stating it was an accident. Central Intelligence Agency (CIA) Director George Tenet testified before a congressional committee that the bombing was the only one in the campaign organized and directed by his agency, and that the CIA had identified the wrong coordinates for a Yugoslav military target on the same street. The Chinese government issued a statement on the day of the bombing, stating that it was a "barbarian act".In October 1999, five months after the bombing, The Observer of London along with Politiken of Copenhagen, published the results of an investigation citing anonymous sources which said that the bombing had actually been deliberate as the Embassy was being used to transmit Yugoslav army communications. The governments of both the U.S. and the U.K. emphatically denied it was deliberate, with U.S. Secretary of State Madeleine Albright calling the story "balderdash" and British Foreign Secretary Robin Cook saying there was "not a single shred of evidence" to support it. In April 2000 The New York Times published the results of its own investigation for which, "the investigation produced no evidence that the bombing of the embassy had been a deliberate act."Right after the bombing, most Chinese believed it was deliberate and many continue to believe that it was deliberate; however, in the results from structured interviews conducted in 2002, of the 57% of Chinese Sino-American relations experts who believed that the bombing was deliberate, 87.5% did not suspect President Clinton's involvement.In August 1999 the United States agreed to compensate the victims of the bombing and their families. In December 1999 the United States agreed to pay China for the damage to the embassy and China agreed to compensation to the United States for damage to U.S. property that occurred during the demonstrations.In May 2000 a major U.S.-China trade bill passed the United States House of Representatives which became the United StatesChina Relations Act of 2000 integrating with China's entry into the World Trade Organization. By June 2000, during a visit to China by U.S. Secretary of State Madeleine Albright, both sides said that relations between them had improved.

The Kosovo War was an armed conflict in Kosovo that started 28 February 1998 and lasted until 11 June 1999. It was fought by the forces of the Federal Republic of Yugoslavia (i.e. Serbia and Montenegro), which controlled Kosovo before the war, and the Kosovo Albanian rebel group known as the Kosovo Liberation Army (KLA). The conflict ended when the North Atlantic Treaty Organization (NATO) intervened by beginning air strikes in March 1999 which resulted in Yugoslav forces withdrawing from Kosovo.

The KLA formed in the early 1990s to fight against Serbian persecution of Kosovo Albanians. The KLA initiated its first campaign in 1995 when it launched attacks against Serbian law enforcement in Kosovo. In June 1996, the group claimed responsibility for acts of sabotage targeting Kosovo police stations, during the Kosovo Insurgency. In 1997, the organisation acquired a large amount of arms through weapons smuggling from Albania, following a rebellion in which weapons were looted from the country's police and army posts. In early 1998, KLA attacks targeting Yugoslav authorities in Kosovo resulted in an increased presence of Serb paramilitaries and regular forces who subsequently began pursuing a campaign of retribution targeting KLA sympathisers and political opponents; this campaign killed 1,500 to 2,000 civilians and KLA combatants.After attempts at a diplomatic solution failed, NATO intervened, justifying the campaign as a "humanitarian war". This precipitated a mass expulsion of Kosovar Albanians as the Yugoslav forces continued to fight during the aerial bombing of Yugoslavia (March–June 1999). By 2000, investigations had recovered the remains of almost three thousand victims of all ethnicities, and in 2001 a United Nations administered Supreme Court, based in Kosovo, found that there had been "a systematic campaign of terror, including murders, rapes, arsons and severe maltreatments", but that Yugoslav troops had tried to remove rather than eradicate the Albanian population.The war ended with the Kumanovo Treaty, with Yugoslav and Serb forces agreeing to withdraw from Kosovo to make way for an international presence. The Kosovo Liberation Army disbanded soon after this, with some of its members going on to fight for the UÇPMB in the Preševo Valley and others joining the National Liberation Army (NLA) and Albanian National Army (ANA) during the armed ethnic conflict in Macedonia, while others went on to form the Kosovo Police. After the war, a list was compiled which documented that over 13,500 people were killed or went missing during the two year conflict. The Yugoslav and Serb forces caused the displacement of between 1.2 million to 1.45 million Kosovo Albanians. After the war, around 200,000 Serbs, Romani, and other non-Albanians fled Kosovo and many of the remaining civilians were victims of abuse.The NATO bombing campaign has remained controversial. It did not gain the approval of the UN Security Council and it caused at least 488 Yugoslav civilian deaths, including substantial numbers of Kosovar refugees.