From 1999 to 2001, Pardew was the Deputy Special Advisor to the President and Secretary of State for Democracy in the Balkans during the NATO conflict in Kosovo and the subsequent peace settlement. In that capacity, Pardew engaged directly in negotiations over Kosovo with President Slobodan Milošević of Serbia and with a variety of Kosovo political leaders. He was the Washington coordinator for the international Kosovo Verification Mission. Following the successful NATO bombing campaign, Pardew assisted in establishing U.S. and international civilian presences in Kosovo and in the development of local Kosovo institutions of government and security.