For the National Council election in 1999, He was originally expecting a nomination for a ministerial post provided he was in the course of forming a government in 2000 by Federal President Thomas Klestil for perceived as particularly tasteless xenophobic statements during the election campaign rejected. Instead, he was nominated by the Freedom Party, which was the second largest at that time party to the Second National Council President, giving him a few days, however to come up with a campaign. In autumn 2002, it looked as if he should again play a greater role in the party, because in September 2002 he was diagnosed in Linz as the deputy party leader. After the early parliamentary elections in 2002, however, the FPÖ fell back to third place, in the result was Prinzhorn from now third National President. The Entrepreneur and economic spokesman for the Freedom Party was at that time mainly as a support of the government team led by the former Vice-Chancellor and FPÖ chief Susanne Riess-Passer . The relationship with Carinthia's Governor Jörg Haider was against noticeably cooled in the meantime. As part of the intra-party turmoil and its related materiel withdrawal from the FPÖ in 2005, he was still to April 27, 2006 Member of the services of the FPÖ, thereafter for up to 29 October 2006, the BZÖ. The Office of the Third Speaker of Parliament he had held until 30 October.