Far-right National Democratic Party leader Udo Voigt, party spokesman Klaus Beier and the head of the party's legal committee, Frank Schwerdt, face two counts of racial incitement and one of defamation.
The defendants refused to enter pleas in their trial's opening day.
They are said to have printed and distributed leaflets before the 2006 World Cup insinuating that Patrick Owomoyela was not worthy of playing on the German national soccer team.
The NPD distributed the pamphlets in early 2006 ahead of the Germany World Cup showing Owomoyela wearing the white shirt of Germany's national team with the caption, "White. Not just the color of the jersey!"
Owomoyela, the son of a German mother and Nigerian father, has already won a civil trial against the NPD. Following that victory, he and the German Soccer Federation (DFB) also filed criminal charges.
The DFB has said it fully backs its black former national defender, adding it was pressing charges to fight "the racist campaigns against players for the German national team."
Owomoyela currently plays for Borussia Dortmund.
The trial was supposed to have begun in the first week of March, but had to be postponed because the three defendants couldn't be found at their registered addresses.
If found guilty, the three men could each face a fine or up to three years in prison.