But the conference on Sunday almost never convened.
Twice cancelled due to the acute sensitivity of the Armenian question, it has been billed as a litmus test for freedom of expression in Turkey.
Nationalist demonstrators hurled eggs and tomatoes at participants as they arrived at Istanbul's private Bilgi University to discuss claims that Ottoman Turks committed
genocide against Armenians during and after World War I.
Protesters waved Turkish flags and chanted slogans accusing the conference participants of betraying the nation.
But the mere fact that the conference had gone ahead prompted strong praise from local media.
Gul(L): Turks are at peace with
themselves and their history
"Another taboo is destroyed. The conference began but the day of judgement did not come," said the Milliyet daily.
The liberal Radikal newspaper took a similar line.
"Even the word 'genocide' was uttered at the conference, but the world is still turning and Turkey is still in its place," its front-page headline said.
"Free discussion, free protest," said Turkey's top-selling Hurriyet newspaper, noting that both conference participants and demonstrators were freely expressing their opinions.
Armenia and its supporters around the world say about 1.5 million Armenians perished in a systematic genocide committed by Ottoman Turkish forces between 1915 and 1923.
Ankara accepts that many Armenians were killed on Turkish soil, but says they were victims of a partisan conflict that claimed even more Turkish Muslim lives as the Ottoman Empire was collapsing. It denies any genocide.
In a message to the conference, Foreign Minister Abdullah Gul expressed Turkey's official view that many citizens of the Ottoman Empire suffered terribly during the war, but that claims of an Armenian genocide were false and politically motivated.
The conference was twice
cancelled due to sensitivities
"The Turkish people are at peace with themselves and with their history," Gul said.
Deniz Baykal, leader of Turkey's main opposition Republican People's Party, said on Sunday he thought the conference was too one-sided in its approach to the Armenian issue, but he defended the right of academics to debate freely.
The conference had originally been scheduled for May but was cancelled after a government minister accused those backing Armenian genocide claims of "stabbing Turkey in the back".
After a storm of criticism from the EU and elsewhere, the government agreed to let the conference go ahead, but a last-minute court order prevented it from opening on Friday, to Prime Minister Tayyip Erdogan's acute embarrassment.
"Even the word 'genocide' was uttered at the conference, but the world is still turning and Turkey is still in its place"
Radikal newspaper headlin
The organisers then circumvented the court ban by moving the two-day conference to a third venue, Bilgi University. It opened on Saturday to noisy nationalist protests.
Despite a flurry of EU-inspired liberal reforms in recent years, promoting certain interpretations of Turkish history can still be deemed a criminal offence under the revised penal code.
Turkey is due to begin EU entry talks on 3 October, though it is not seen as joining the bloc before 2015 at the earliest.