In a speech that was carried live on Al-Jazeera and Al-Arabiya, President Obama told members of the Turkish Parliament that the United States "is not at war with Islam" and called for a stronger relationship between the United States and the Muslim world that goes beyond the fight against al Qaeda.
"I know there have been difficulties these last few years," Obama said, in what is just the latest nod to an apology for the Bush years that Obama has made in first presidential overseas trip.
"I know that the trust that binds us has been strained, and I know that strain is shared in many places where the Muslim faith is practiced. Let me say this as clearly as I can: The United States is not at war with Islam," the president said.
Turkey is the last stop on Obama's European swing and his first visit to a Muslim nation as president. He firmly expressed his commitment for the European Union to accept Turkey as a member, praised progress the majority-Muslim country has made on human and minority rights and suggested that Turkey has a unique role in helping to broker peace around the world.
Obama said the partnership between the United States and the Muslim world is critical in the fight against Islamic terrorism, what he called "a fringe ideology that people of all faiths reject."
But he also said the partnership has to be about more than just fighting global terrorism.
"I also want to be clear that America's relationship with the Muslim world cannot and will not be based on opposition to al Qaeda. Far from it," he said.
On this final leg of his first overseas trip, Obama sought to repair relations with the Muslim world that were damaged after the attacks of Sept. 11 and the war in Iraq. The president said his administration seeks "broad engagement based upon mutual interests and mutual respect."
"We will listen carefully, bridge misunderstanding and seek common ground. We will be respectful, even when we do not agree," he said. "And we will convey our deep appreciation for the Islamic faith, which has done so much over so many centuries to shape the world for the better -- including my own country."
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Obama noted his personal ties to the Muslim world and the connection that many Americans have.
"The United States has been enriched by Muslim Americans. Many other Americans have Muslims in their family or have lived in a Muslim-majority country. I know because I am one of them," said Obama who lived for several years as a child in Indonesia.
Obama said earlier today that his trip to Turkey, a majority-Muslim nation, was intended to send a message.
"I am trying to make a statement about the importance of Turkey not just to the United States but to the world. This is a country that has been often said lies in the crossroads between East and West," Obama said during a news conference with Turkish President Abdullah Gul.
Obama said that as a member of NATO and a majority Muslim nation, Turkey is in a unique position and "has insights into a whole host of regional and strategic challenges that we face."
Obama indicated he wanted to move beyond military issues in the U.S.-Turkish relationship and look at ways to expand trade and commerce between the two nations.
"It gives me confidence that moving forward, not only are we going to be able to improve our bilateral relations, but as we work together, we're going to be able to, I think, share a set of strategies that can bridge the divide between the Muslim world and the West. That can make us more prosperous and secure."
Earlier today, Obama sidestepped a question about his views on the sensitive topic of whether Turkey should recognize the accusation that the Ottoman Empire committed genocide against the Armenian people during and after World War I.
During the 2008 presidential campaign, Obama said, "The Armenian genocide is not an allegation" and supported the passage of a congressional resolution recognizing the Armenian genocide.
Obama was asked today whether he had changed his stance and whether he urged Gul to acknowledge the genocide.
"My views are on the record and I have not changed my views," the president said, avoiding the word "genocide."
"What I have been very encouraged by is news that under President Gul's leadership, you are seeing a series of negotiations, a process, in place between Armenia and Turkey to resolve a whole host of longstanding issues, including this one."
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In his speech to parliament, Obama said it was not about his views, but how the Turkish and Armenian people "deal with the past."
"The best way forward for the Turkish and Armenian people is a process that works through the past in a way that is honest, open and constructive," he said.
Obama said the United States "strongly supports" Turkey's bid to join the European Union, a statement that earned him a round of applause from the members of parliament.
Obama took a moment to express his condolences for the victims of the earthquake in Italy.
"We just heard the news of the earthquake in Italy and we want to send our condolences to the families there and hope that we are able to get the rescue teams and that we can minimize the damage as much as possible moving forward," the president said.
Earlier today, Obama placed a wreath at the tomb of Mustafa Kamal Ataturk, the founder and first president of the Turkish Republic, inside the Ataturk mausoleum and signed the guest book.
Obama, who is left-handed, held notes in his right hand as he signed the guest book.
"I am honored to pay tribute to Mustafa Kamal Ataturk, a man who vision, tenacity and courage put the Republic of Turkey on the path of democracy and whose legacy continues to inspire generations around the world. As the 44th president of the United States of America, I look forward to strengthening relations between the U.S. and Turkey and supporting Ataturk's vision of Turkey as a…prosperous democracy giving hope to its people and providing 'peace at home, peace in the world.'"
He signed the note "Barack Obama."
ABC News' Stephanie Smith contributed to this report.