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President Barack Obama highlighted the role of Muslims in the United States during his first visit as president to a US mosque on Wednesday and warned that the targeting of religious minorities has no place in US society.

"We're one American family," Obama said in remarks at the Islamic Society of Baltimore.

Attacks against Muslims tear at the fabric of US society and constitutional guarantees of freedom of religion, Obama said.

"We've got to tackle this head on," he said.

Although Obama has spoken vocally about the need for tolerance for Muslims in the past, including after a terrorist attack in San Bernardino, California, in December, it was the first time he had done so at US mosque.

Obama, a Christian, has been faced allegations since his 2008 campaign that he was secretly a Muslim as the son of a Kenyan Muslim father coupled with allegations that he was not actually a US citizen. Obama joked during his remarks that US founding father Thomas Jefferson, who was a strong advocate for religious freedom, had also faced similar allegations.

Rhetoric conflating terrorism and the beliefs of an entire faith "has no place in our country," Obama said amid rising anti-Muslim sentiment and remarks from Republican candidate Donald Trump calling for Muslims to be kept out of the United States.

The president painted a broad historic picture of Muslims' role in the United States since the founding of the country and their ongoing contributions to American society.

He acknowledged however a small fraction of extremists have perverted the religion and created "tensions that overwhelmingly burden majority of Muslims."

Obama called for Americans to refuse to be divided along religious lines and "reaffirm we are all God's children."

Pointing to the US Constitution's guarantee of freedom of religion, he said believers of all faiths must speak up when another faith is attacked, ensure hate crimes are punished and condemn hateful rhetoric.

The US must also not reinforce ideas put forward by Islamic State and other terrorist groups that the US is at war with Islam.

"I refuse to give them legitimacy. We must never give them that legitimacy," he said.

Obama also called on Muslims around the world to reject extremist ideologies and speak out against extremism that has had the most impact on Muslim communities.

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