In March 1997, United Nations Secretary General Kofi Annan appointed Prendergast Under-Secretary-General for Political Affairs at the United Nations and Prendergast served in that position until July 2005. He helped call attention to human rights violations and "ethnic cleansing" resulting from the War in Darfur, and was deeply involved in Cyprus reunification negotiations in 2004, following the Cypriot Annan Plan referendum. He was determined that a solution could be found to problems in Somalia. When he retired in 2005, following pressure from the Bush administration for the removal of key UN Secretariat officials who had opposed the Iraq war and the many subsequent errors of policy, Kofi Annan thanked him for his "outstanding service" and "invaluable advice." He was succeeded by Ibrahim Gambari.