The charges were brought after he led a chant for fewer Moroccans in the Netherlands at a rally 18 months ago.
Mr Wilders, leader of the Dutch Freedom Party (PVV), said the trial at Schiphol, was political and "a travesty".
If convicted, he faces a fine and a year in prison.
Mr Wilders has repeatedly criticised Islam, calling for the Koran to be banned and for the closure of all mosques in the Netherlands.
The trial, in a high-security courtroom, heard that 6,474 complaints had been made in response to Mr Wilders' remarks at a rally in 2014. A sample of 35 complaints was read out.
Prosecutors argued that Geert Wilders crossed a line when he asked supporters if they wanted "fewer or more Moroccans" in the Netherlands.
After supporters chanted back "fewer", he replied: "We'll organise that."
Mr Wilders denounced the trial as an attempt to suppress freedom of speech.
"This is a political process, and I refuse to co-operate with it. We have to talk about politics in parliament, not in the courtroom," he said in a statement read by his lawyer.
But the prosecutor insisted Mr Wilders was wrong to assume that as a politician his remarks were exempt from laws on hate speech.
In 2011, Mr Wilders was acquitted of incitement after being accused of encouraging hatred towards Muslims.
The latest trial comes as opinion polls suggest the PVV is consistently faring well in polls, ahead of parliamentary elections in March.
The party is currently second, behind Prime Minister Mark Rutte's liberal VVD, and is predicted to win 23 seats in the 150-seat parliament.
Dutch anti-Islam politician Geert Wilders has failed to turn up for a trial where he is charged with racial discrimination and inciting hatred.