Many human rights groups criticised civilian casualties resulting from military actions of NATO forces in Operation Allied Force. Both Serbs and Albanians were killed in 90 Human Rights Watch-confirmed incidents in which civilians died as a result of NATO bombing. It reported that as few as 489 and as many as 528 Yugoslav civilians were killed in the NATO airstrikes. Kenneth Roth, the executive director of Human Rights Watch, criticized NATO's decision to bomb civilian infrastructure in the war. "Once it made the decision to attack Yugoslavia, NATO should have done more to protect civilians," Roth remarked. "All too often, NATO targeting subjected the civilian population to unacceptable risks". Yugoslav government estimated that no fewer than 1,200 civilians and up to 2,500 civilians were killed and 5,000 wounded as a result of NATO airstrikes.

From the beginning of Operation Allied Force, NATO pledged to minimise civilian casualties. Consideration of civilian casualties was incorporated into NATO's planning and targeting process. Targets were "looked at in terms of their military significance in relation to the collateral damage or the unintended consequence that might be there", according to General Henry Shelton, Chairman of the Joint Chiefs of Staff. Critics of the campaign have suggested that incidents were the inevitable result of NATO's policy of restricting its pilots to bombing from 15,000 feet or above for the sake of avoiding NATO deaths.