Wilders's Party for Freedom (PVV) came second only to the Christian Democrats (CDA) of Jan Peter Balkenende, the Netherland's prime minister, which won only 20 per cent of the vote, losing two of its current seven seats in the EU parliament.
"This is a fantastic result," Wilders, a controversial figure in Dutch politics who faces a hate speech trial at home, said.
"I hope we will do even better in national elections and that we become the biggest party in the Netherlands."
The PVV opposes the European parliament's very existence, with Wilders having told a newspaper the party was taking part to "bring it down from the inside".
Over 375 million people are eligible to take part in the elections, but voter turn out so far has been low.
Friday's exit polls showed turnout was down at 36.5 per cent from 39.1 per cent in the previous elections in 2004.
The vote, the biggest-ever transnational elections, is expected to be tempered by voter apathy and a focus on national problems rather than European perspectives.
For this very reason, parties on the extremes of Europe's political right and left hope to pick up more seats.
Mario Telo, who heads the European Studies Institute at Brussels Free University, said: "Corruption, scandals and the quest for scapegoats risk bogging down European democracies, which will have to find the strength to react."
In Britain, public outrage over a string of revelations over dubious expenses claims by politicians and a spate of ministerial resignations has put Gordon Brown, the prime minister, under particular pressure.
EU voter turnout has fallen with each election since the first in 1979, despite the growing role the parliament plays in adopting, amending or rejecting laws in Europe.
Ireland and the Czech Republic go to the polls on Friday.
Cyprus, Latvia, Malta and Slovakia will go to the polls on Saturday before Europe's "Super Sunday" - when the other 19 EU nations, including France, Germany, Italy and Spain, round off the voting.
Overall, the European People's Party (EPP) - an umbrella group for centre-right parties from across the EU - looks set to remain the biggest political bloc in the parliament.
Despite the loss of the British and Czech Conservatives, who quit the EPP, deeming it too europhile, the bloc looked set to win 262 seats and 35 per cent of votes cast, according to the final pre-election opinion poll.