In 1990-1992, Vondra was foreign policy advisor to President Václav Havel. When Havel stepped down from his office during dissolution of Czechoslovakia and at the same time independent Czech foreign service began to be formed, Vondra became 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 preparation of 2002 Prague summit of the NATO. From January to July 2003 Vondra was a Deputy Foreign Minister. He became an ODS member only after his ministerial appointment and the victory in Senate elections in October 2006. He is generally perceived as pro-United States and wary of European integration though less than ODS eurosceptic hardliners, and had good connections to Havel . Vondra was mentioned as a possible nominee to serve as European Commissioner in 2009. He participated at the international conference European Conscience and Communism, which took place under his patronage at the Czech Senate in Prague in June 2008. In November 2012, he decided to step down from politics, due to the loss of credibility following several corruption accusations and his previous relentless effort to pursue an installation of a US military missile radar, despite the prevailing opposition of his fellow Czech citizens. In 2019 Vondra returned to politics when the Civic Democratic Party nominated him in European Parliament election. He was on 15th place on party's list. He received 29,536 preferential votes and was elected. Vondra then ran for the position of Vice-Chairman of ODS. He received 443 votes of 502 which was more than any other candidate and was elected.
He is married and has 3 children with his wife Martina: Vojtěch, Anna and Marie. He has another child, Jáchym, with Veronika Vrecionová.
Trivia
In 2014, he rejected Noam Chomsky's statements about dissidents in the East Europeancommunist countries, and remarked that "at the time when people like Havel were in Communist jails over their fight for freedom, Chomsky advocated Pol Pot's genocide in Cambodia from the Boston cafes" and he warned that if the world listens to "rubbish from these people" it will once again lead to concentration camps and gulags.