In the Verhofstadt I Government Antoine Duquesne served as the Federal minister of the interior (1999–2003). In 2003–2004 Duquesne served as President of the MR. In 2003 Duquesne was elected to the Senate once more, served as Chairman of the Senate's Committee on Agriculture and Small Businesses, but he resigned in 2004 upon election to the European Parliament, in which he served 2004–2009. He sat on the European Parliament's Committee on Civil Liberties, Justice and Home Affairs and was a substitute for the Committee on Constitutional Affairs, a vice-chair of the Delegation for relations with Mercosur and a substitute for the Delegation to the EU-Bulgaria Joint Parliamentary Committee.