"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," Obama said during an address to Turkish lawmakers.
Obama called Turkey a critical U.S. ally, saying the two countries must work and stand together to overcome the challenges facing the world today.
"The United States and Turkey have not always agreed on every issue," he said. "But we have stood together through many challenges over the last 60 years."
Although addressing lawmakers, Obama also spoke to the Muslim world at large, speaking of peace negotiations with Israel and Palestine, the emerging democracy in Iraq, terrorist acts by al-Qaida and the Taliban in Afghanistan and Pakistan, and the potential nuclear threat in Iran.
But, he said, "America's relationship with the Muslim world cannot and will not be based on opposition to al-Qaida. ... We seek broad engagement based upon mutual interests and mutual respect. We will listen carefully, bridge misunderstanding and seek common ground."
The United States supports Turkey's bid to become a member of the European Union. Turkey already is a member of NATO and the Group of 20.
Earlier, Obama honored modern-day Turkey's founding father, Mustafa Kemal Ataturk, participating in a wreath-laying ceremony at Ataturk's tomb in Ankara.