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To make matters even more difficult for him, the turnout was high at 53.1 percent of the electorate. Previously, the Yes campaign had indicated that if the turnout was high it would help their campaign, while a low turnout would cause them difficulties.
Ireland's rejection of the Lisbon Treaty leaves the EU facing a crisis similar to that which followed the 2005 rejection of the formal constitution. It also means that three million voters have effectively decided the fate of a bloc of almost 500 million people.
Ireland has caused upsets in EU referendums before. In 2001, its voters rejected the Nice Treaty, a result overturned in a second poll the following year.
Backers of the treaty, which aims to make EU decision-making more efficient, struggled to get their message across, despite a campaign backed by all bar one of the main political parties.
Opponents rallied support for the No campaign around claims including that the treaty threatens sensitive Irish policies like the ban on abortion, low corporation tax and military neutrality.
Elsewhere in Europe there has been some bemusement that a country which owes its economic success - as the Celtic Tiger of the 1990s - largely to massive European Union investment should reject closer European ties.
Libertas, a group run by the businessman Declan Ganley and the Sinn Fein party, led by Gerry Adams, were among the most prominent 'no' campaigners.
Mr Ganley said today: "The Irish people should never have been taken for granted. In their enormous wisdom they have taken on board the treaty, looked at the arguments and, it seems that we have returned the same result again that our fellow Europeans in France and the Netherlands have already sent to the unelected Brussels elite."
He added: "In fairness to Mr Cowen and the Yes side they did everything they could - including some off-the-ball tackles - to get the result that Brussels wanted, so nobody should criticised him from there.
"But what this does is to give Mr Cowen a mandate to go back to Brussels and build a better deal. I have faith in him that he will do that."
In a sign of the passions aroused by the issue, Brian Lenihan, the Finance Minister, had to be escorted from Dublin's main counting station when No campaigners attempted to drown him out and scuffles broke out. "As you know from Eastern Europe when the Far Right and the Far Left take over free speech disappears very fast," he said.
Mr Lenihan told The Times: "The trend is not favourable. I am disappointed with the result. Clearly Ireland is not in a position to ratify the treaty. We will await the reaction of other member states.
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