The stability of the young state was gravely tested during the 1999 Kosovo crisis, when Macedonia temporarily hosted about 360,000 refugees from the violence and ethnic cleansing in Kosovo, as Serb atrocities against Kosovar Albanians and other minority groups caused a mass exodus. The refugee influx put significant stress on Macedonia's weak social infrastructure. With the help of NATO and the international community, Macedonia ultimately was able to accommodate the influx. Following the resolution of the conflict, the overwhelming majority of refugees returned to Kosovo. The Macedonian Government demonstrated a strong commitment to regional stability as an essential partner during the Kosovo crisis.

In addition to improving relations with its neighbors, Macedonia has made strides toward European and international integration, especially with the EU and NATO. Macedonia is an active participant in NATO's Partnership for Peace and Membership Action Plan, the OSCE, and United Nations, and was accepted as a member of the World Trade Organization (WTO) in October 2002. In May 2003, Macedonia, Albania, Croatia, and the U.S. created the Adriatic Charter , modeled on the Baltic Charter, as a mechanism for promoting regional cooperation to advance each country's NATO candidacy.

In 1999, the EU agreed to develop a Stabilization and Association Agreement (SAA) with Macedonia; negotiations with Macedonia were launched April 5, 2000. The SAA was signed April 2001 and came into force in April 2004. Its trade and trade-related provisions have been in force since June 2001. For Macedonia to successfully integrate within the global arena, continued efforts to strengthen its multi-ethnic civil society institutions, to develop measures to promote economic growth and investment, and to foster strong indigenous non-governmental organizations are necessary. On November 9, 2005 the European Commission issued an "avis" on Macedoniaís EU membership candidacy in which it recommended EU candidate status for the country. It recommended beginning formal accession negotiations after Macedonia has made further progress on a number of reform fronts, including combating corruption; enacting judicial, administrative, and economic reforms; and conducting free and fair parliamentary elections, in accordance with European standards, in 2006.