The reasons for the shooting are not clear, but Major Nidal Malik Hasan was reported to be unhappy at the alleged abuse he had received. US Army Major Nidal Malik Hasan was due to be deployed to Afghanistan.
The BBC's Penny Spiller considers how it may affect the thousands of Muslims in the US military.
Major Nidal Malik Hasan is a career soldier with some 20 years experience, who had trained as a psychiatrist and treated troops returning from combat.
He is also reported to be a devout Muslim, who attended daily prayers at a mosque and was seen on the morning of the shooting wearing traditional Arabic dress as he shopped for groceries.
His relatives said he had become disillusioned with US military operations in Iraq and Afghanistan, and strongly opposed his own imminent deployment to Afghanistan.
He had also long wanted to leave the army after suffering harassment because of his religion, they said.
Whatever the motivation, the tragedy at Fort Hood army base highlights the sensitivities surrounding the issue of American Muslims serving in the US armed forces.
Kamran Memon of the organisation Muslims For a Safe America says the subject splits America's Muslim community down the middle.
"Those at one end of the spectrum say we should have nothing to do with the US armed forces as they are involved in wars with our fellow Muslims abroad," he told the BBC.
"Those at the other end say we should definitely serve and help defend our country against those who wish to attack it.
"There is no easy answer to this. We are trying to encourage American Muslims to learn about these issues and use their critical thinking skills to reach informed conclusions so that we can become greater participants in the debate about national security issues."
Mr Memon says the vast majority of Muslim citizens in America are "able to live peaceful lives", even though they have probably suffered some discrimination, if only a hostile look, since the 11 September 2001 attacks.
He believes that this will also be true of those Muslims who serve in the US armed forces.
However, there have been some high profile incidents in recent years that have fuelled tensions.
At a camp in Kuwait, as his unit prepared to move into Iraq in March 2003, Sergeant Hasan Akbar threw hand grenades and opened fire on a tent full of sleeping soldiers in the early hours of the morning.
He killed two officers Air Force Major Gregory Stone and Army Captain Christopher Scott Seifert) and injured 14 other personnel 101st Airborne Division.
His family said he had been suffering religious and racial harassment from other soldiers, although no witnesses were provided at his trial. The prosecution described him as a "hate-filled, ideologically driven murderer".
Also in 2003, a Muslim chaplain at Guantanamo Bay, Captain James Yee, was accused of espionage and kept in solitary confinement for 76 days before all the charges were dropped.
He was given an honourable discharge - but not an apology - from the army a year later. The case outraged Muslim Americans who felt Captain Yee had been singled out because of his religion.
It is not clear exactly how many Muslims serve in the 1.4 million-strong US armed forces, as recruits are not required to state their religion.
"We have a diverse armed forces, and whatever their religion our troops have a part to play, and they play it very well," Lt Col Nathan Banks, Army spokesman
According to the Pentagon, there are 3,572 Muslims in active service. However, some Muslims in the military say the real number is as high as 20,000.
The US government has made no secret of the fact that it would like to see more people from Arab and Muslim communities joining the armed forces.
More American Muslim troops on the ground in Iraq and Afghanistan has long been seen as a vital part in helping the US in its missions to win hearts and minds in those countries.
"They are a great asset to the army," Lt Col Nathan Banks, army spokesman for the Pentagon, told the BBC.
"When they do deploy they help facilitate a lot of our missions. American Muslims in the army work hand in hand with local Muslims, and we welcome that."
He said the army did not foresee heightened tensions within its ranks as a result of Fort Hood.
"This was an isolated incident. Our hearts go out to everyone affected by this, but the army will stay strong. We have a diverse armed forces, and whatever their religion our troops have a part to play, and they play it very well."
But anti-Muslim sentiment is being felt as a result of the shooting. The Arab-American Institute - which condemned the massacre - said it had received at least one threatening phone call, and expected more.
One soldier at the Texas base admitted the coming days would be tough for his Muslim colleagues.
"They've taken it hard due to the fact that it kind of puts a negative light on them and makes people distrust them," he told the BBC.
"Because everybody is going to look at them [and think]: "Well, you're probably going to pull something like this. And it's a sad fact that that will happen".