Shortly before the 1989 election, Juncker was seriously injured in a road traffic accident, spending two weeks in a coma. He nonetheless recovered in time to be returned to the Chamber of Deputies once more, picking up the Finance portfolio along with his Ministry of Labour post. The Ministry of Finance post is traditionally seen as a rite of passage to the premiership of the country, and his eventual promotion to Prime Minister seemed at this time inevitable, with political commentators concluding that Santer was grooming Juncker as his heir. Juncker at this time accepted the position of Governor of the World Bank.
Juncker was re-elected to the Chamber in 1994, maintaining both his ministerial roles. With Jacques Santer ready to be nominated as the next President of the European Commission, it was only six months later, on January 20, 1995, that Grand Duke Jean approved the appointment of Juncker as Prime Minister, as part of a coalition with the Luxembourg Socialist Workers' Party. Juncker relinquished his post at the World Bank at this time (swapping it for governorship of the International Monetary Fund) but maintained his previous ministerial positions; he was now the Minister of State, of Labour and Employment and of the Treasury.
1997 brought the rotating Presidency of the European Council to Luxembourg for the first time in Juncker's administration, giving Juncker a bigger stage on which to pitch his pro-European proposals. Juncker championed the cause of social integration in Europe, along with constituting the so-called "Luxembourg Process" for integrated European policy against unemployment. He also instigated the "Euro 11", an informal group of European finance ministers for matters regarding his Economic and Monetary Union ideals.
Juncker succeeded in winning another term as Prime Minister in the 1999 elections, although the coalition with the Luxembourg Socialist Workers' Party was broken in favour of one with the Democratic Party. After the 2004 elections, the Luxembourg Socialist Workers' Party became the second largest party again, and Juncker again formed a coalition with them. Shortly after re-election, Juncker found himself misinformed at a European Union summit over the condition of then-ailing Palestinian National Authority leader Yasser Arafat. Juncker mistakenly announced his death prematurely, before retracting the claim citing misunderstanding.
In 2005, Juncker inherited a second term as European President, but this six-month chairmanship was dogged by infighting in European circles; at one point, during a visit to Brussels by the United States President George W. Bush, he famously claimed that "if ridiculousness could kill, the streets of Brussels would be piled high with dead bodies." There were complications also in ratification of the European Constitution treaty, with France voting against the proposal on May 29 and the Netherlands following suit three days later. Shortly after the expiration of his term came Luxembourg's referendum on ratification, and Juncker staked his political career on its success, promising to resign if the referendum failed. The final result was a 56.5% Yes vote on an 88% turnout. His continued allegiance to European ideals earned him the 2006 Karlspreis.
Juncker is currently the longest-serving head of government of any European Union state. It is often suggested in the press that he, like his predecessor Santer, will eventually give up his position as Prime Minister to assume the presidency of the European Commission, but Juncker continues to deny he has any plans to resign.
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