After Helmut Kohl lost his bid for a fifth term in the 1998 federal election, in the opposition Seehofer became deputy chairman of the CDU/CSU parliamentary group of the Bundestag in October 1998, which was led at the time by Kohl's successor Wolfgang Schäuble. He served as Health Minister Ulla Schmidt's counterpart in negotiating the cross-party healthcare bill of 2003. Because of his disagreement with CDU leader Angela Merkel on flat-rate contributions ("Gesundheitsprämie") to the federal health insurance he resigned from his leadership post in the parliamentary group on 22 November 2004 but remained deputy chairman of his party and kept his Bundestag seat.