In 1990-1992, Vondra was foreign policy advisor to President Václav Havel. When Havel stepped down from his office during the dissolution of Czechoslovakia and at the same time an independent Czech foreign service was being formed, Vondra became the Czech Republic's First Deputy Minister of Foreign Affairs in August 1992, responsible i. a. for negotiating the division of Czechoslovak diplomacy. In 1996 he was a chief negotiator for the Czech-German Declaration on the Mutual Relations and their Future Development. In March 1997 Vondra left to become the Czech Ambassador to the United States, staying there until July 2001. From March 2001 to January 2003, Vondra was the Czech Government Commissioner responsible for the preparation of the 2002 Prague summit of NATO. From January to July 2003 Vondra was a Deputy Foreign Minister.