The unfolding saga has riveted a country where a crackdown on elected politicians has not been seen since a military coup nearly five decades ago.
Mihaloliakos has denied the charges against him. He was arrested on Saturday alongside other party members as part of the government's efforts to rein in a party it says is a neo-Nazi criminal gang. The party rejects the neo-Nazi label.
"Long live Greece, victory," Mihaloliakos said as he left the court.
His wife and daughter, joined by other Golden Dawn lawmakers, waited outside the court during a rainy night for the outcome of the hearing. "You are a diamond, don't buckle," she told him.
(Read More: Greece: 'Tourism bonanza' to give economy a boost?)
Earlier, as Mihaloliakos was brought to court by police, about 200 party supporters carrying Greek flags shouted, "Blood, honor, Golden Dawn."
Another party member was also detained pending trial after responding to the same charges, the court official said.
On Wednesday, three senior Golden Dawn lawmakers were freed pending trial on the same charges in an unexpected setback to the government's efforts to clamp down on the party.
The decision to free the three men after an 18-hour court session raised questions about the state's case against Golden Dawn after one of its sympathizers stabbed to death an anti-fascism rapper.
(Read More: Greek police arrest leader of Golden Dawn party)
Party spokesman Ilias Kasidiaris and fellow lawmakers Ilias Panagiotaros and Nikos Michos stormed out of the court to cheers of "Bravo" from supporters. They kicked and shoved journalists out of the way before hailing a taxi.
Golden Dawn rose from being a fringe party to win 18 seats in parliament in last year's election. It has drawn on anger over the debt crisis, budget cuts, high unemployment and corruption to become what opinion polls indicate is Greece's third most popular party.
But the latest polls show it has lost about a third of its support since the killing.
Another senior Golden Dawn lawmaker, Christos Pappas, will face the magistrates later on Thursday to respond to the charges.