President Barack Obama gave a rallying cry in defence of religious liberty today during his first visit to a US mosque since he was elected president.

He spoke at the Islamic Society of Baltimore mosque in Maryland this afternoon, emphasising the importance of religious freedom and celebrating the contribution of Muslim Americans.

"This mosque, like so many across this country, is part of the American story," Obama told those gathered. "It's been part of this city for nearly half a century, serving thousands of families. A lot of Americans have never visited a mosque, and to those watching this today who haven't, think of your own church or synagogue, or temple, and a mosque like this will be familiar to you.

"It's where families come to worship and express their love for God and each other."

Obama praised the contribution of Muslims all across the US. "The first thing I want to say are two words Muslim Americans don't hear enough," he said. "Thank you".

"For serving your communities, for lifting up the lives of your neighbours and helping keep us strong and united as one American family. We are grateful for that."

The president acknowledged that for many Muslims, this was a time of anxiety and fear. "Like all Americans, you're worried about the threat of terrorism, but on top of that, as Muslim Americans, you also have another concern: your entire community so often is the target of blame for violent acts of the very few."

The media often gives a distorted impression of the Muslim community, he said, and it's time for Muslims to be better represented, both in the news and on television.

Obama also pointed to the "inexcusable political rhetoric against Muslims", which he said has "no place in our country".

Referring to letters he's received from Muslims saying that they have been made to feel like second-class citizens, he said this: "We're one American family". When any individual feels targeted because of their faith, "it tears at the very fabric of our nation," he added.

"We have to be honest and clear about it, tackle it head on and speak out."

People of all faiths must also reaffirm a "fundamental truth: we are all God's children, we are all born equally with inherent dignity," Obama said. "Christians, Jews and Muslims, we are all under our faiths descendants of Abraham, so mere tolerance is not enough. Our faiths summon us to embrace our common humanity... All of us have the task of expressing our religious faith in a way that seeks to build bridges rather than to divide."

Obama said that Islam has a long history in America, as many of the slaves brought over from Africa were Muslim. He also pointed to previous presidents having expressed the importance of religious freedom, including Thomas Jefferson and John Adams. He noted that Jefferson, like himself, was accused of being a Muslim. "I'm in good company," he joked.

"So this [the Muslim American community] is not a new thing," he said. "Generations of Muslims have helped to build our nation."

There are Muslims in the American army, in the emergency services and in homeland security, he said. "Muslims enrich our lives today in every way".

However, he also highlighted Islamist groups that have appropriated the faith for their own gain. "Even as the overwhelming majority of the world's Muslims embrace Islam as a source of peace, it is undeniable that a small fraction of Muslims propagate a perverted interpretation of Islam," Obama said.

"This is the truth. Groups like al-Qaeda and ISIL are not the first extremists in history to misuse God's name – it's been seen before across all faiths. But right now there is an organised extremist element that draws from Islamic texts and twists them in an attempt to justify killing and terrorism".

The question for all of us, Obama said, is how to move forward "and keep this country strong and united, and defend ourselves against organisations that are bent on killing innocents".

People of all faiths and none must work together to combat extremism, he said. Muslim leaders must speak out against groups like Islamic State, but everyone must actively work to counter Islamophobia.

"If we're serious about religious freedom, and I'm speaking to my fellow Christians who remain a majority in this country, we have to understand that an attack on one faith is an attack on all our faiths," Obama said. "And when any religious group is targeted we have to speak up."

"We have to reject a politics that seeks to manipulate prejudice or bias... We have to be consistent in condemning hateful rhetoric and violence against everyone, including Muslims in the United States of America.

"None of us can be silent. We can't be bystanders to bigotry. Together, we have got to show that America truly protects all faiths."

This is vital in combating the rhetoric of extremists, who claim that Muslims must choose between their faith and their US citizenship, the president added. Speaking directly to young people, he warned them not to believe messages that tell them they have to choose between their identities. "If you're ever wondering 'how do I fit in here?', as President of the United States, I say you fit in here. Right here. [This is] right where you belong... you're not Muslim or American, you're Muslim and American".

Obama also addressed criticism he's received for not denouncing Islam as a violent faith in light of the rise of groups such as ISIS. "The best way for us to fight terrorism is to deny these organisations legitimacy, and to show that here in the United States of America we don't suppress Islam, we celebrate and lift up the successes of American Muslims," he said.

To do otherwise would be to "play into terrorist propaganda" he warned.

Speaking to American Muslims, he said: "To use a little Christian expression: let your light shine. Because when you do, you'll make it clear that this is not a clash of civilisations between the West and Islam. This is a struggle between the peace-loving overwhelming majority of Muslims around the world and a radical tiny minority".

"We've got to build trust and mutual respect, to keep our communities strong and united," he added.

Obama concluded with a call for unity across the US. "We are one family. We will rise and fall together. It won't always be easy, there will be times where our worst impulses are given voice, but I believe that ultimately our best voice will win out. And that gives me confidence and faith in our future," he said.

"After more than 200 years, our blended heritage, the patchwork quilt of America, is not a weakness, it's one of our greatest strengths and what makes us a beacon to the world... May God's peace be upon you, and God bless the United States of America."

Today was not the first time Obama has visited a mosque, having been to several during official trips abroad, but he has waited until his eighth and final year of presidency to visit a mosque in the US.

The aim of the visit, according to the White House, was to "reiterate the importance of staying true to our core values – welcoming our fellow Americans, speaking out against bigotry, rejecting indifference, and protecting our nation's tradition of religious freedom."

The White House described the visit as timely, particularly in the context of the anti-Islamic rhetoric present in the election campaign. However, some Muslim groups have voiced their frustration that it has taken Obama eight years to visit an Islamic place of worship in America.

"I do think it should have happened a long time ago," said Haroon Moghul, a fellow at the Institute for Social Policy and Understanding.

"I don't know why he has not visited a mosque before. If I'm being charitable, I would say it may just not have been a priority. Another reason is the optics may have caused him some grief, but that's precisely why he should have gone in view of the current climate."

There has been an increased number of attacks on US mosques and individual Muslims – who make up around one per cent of America's population – since the Paris attacks in November and a shooting in San Bernardino in December, according to advocacy group Council on American-Islamic Relations (CAIR).

"I don't think there's ever been this level of fear and apprehension in the Muslim-American community," said Ibrahim Hooper from CAIR.

"For some time, we've been asking for pushback. Perhaps this will start a trend."

Obama's visit to the Islamic Society of Baltimore mosque follows his visit to the Israeli embassy in Washington last week, where he warned of growing anti-Semitism.