Editor's note: Peter Bergen is CNN's national security analyst, a director at the New America Foundation and the author of "Manhunt: The Ten-Year Search for bin Laden -- From 9/11 to Abbottabad." Jennifer Rowland is a program associate at the New America Foundation.
(CNN) -- There have been Christians in the Middle East since the time of, well, Christ.
Now that two millennium-long history could be in danger.
Islamist thugs have attacked dozens of churches across Egypt in the past few days, burning many of them down.
The attacks seemed to be protests against the brutal military government crackdown on the Muslim Brotherhood that killed many hundreds of Egyptian Islamists over the past week.
Pope Tawadros II, the leader of Egypt's Christian Copts, met publicly with top military officers as they announced the coup that removed President Mohamed Morsy and his Muslim Brotherhood government from power in early July.
Christians, who make up 10% of the population, and other minorities had complained that a new constitution that had been passed by the Morsy government infringed on their rights.
For some Islamist militants, now it's payback time. According to one report, 52 churches across Egypt were attacked in 24 hours last week. The Egyptian Initiative for Personal Rights has counted at least 30 churches attacked, along with other Christian facilities.
After Morsy was removed from power, a mob armed with axes hacked a Christian businessman to death near Luxor in southern Egypt and then continued their rampage in the village of Nagaa Hassan, burning dozens of Christian homes and killing three other Christians.
Today there are more than 10 million Christians in the Middle East and they make up an estimated 5% of the Middle East's population.
A century ago they made up an estimated 20%.
Much of this fall can be attributed to factors such as emigration and the high birth rates of many Arab Muslims, but some of it is also attributable to the increasing marginalization and targeting of Christians; a worrying trend being seen not just in Egypt but also in other Arab countries.
Take Syria. Many Syrian Christians have tacitly supported the regime of President Bashar al-Assad, which draws much of its strength from the small Shia Alawite sect and therefore has historically favored and protected Syria's other religious minorities.
As a result, the jihadists who have come to dominate a significant portion of the Syrian rebel movement have supplemented their war against the government with attacks that target Christians. On June 27, a suicide bombing in a Christian area of Damascus killed at least four people.
Al Qaeda-affiliated rebels are suspected of killing an Italian priest who had spent most of his life rehabilitating a monastery north of the Syrian capital of Damascus and who disappeared last month. The Rev. Paolo Dall'Oglio had reportedly been trying to secure the release of several hostages in the custody of an al Qaeda-aligned group.
Meanwhile, in March in Benghazi, Libya, where a militant attack on a U.S. government complex left four Americans dead in September 2012, around 60 Christians were rounded up by extremists and handed over to the government on suspicion of immigrating from Egypt illegally. The militants tortured several of their captives, killing one of them.
That bout of vigilantism followed the arrest in February of four Christians accused of proselytizing to Muslim Libyans.
The consequence of such attacks and harassment has been an exodus of Christians from the region.
Residents of northeastern Syria, where Christians have historically been concentrated, estimate that one-third of the Christians there have fled the country during the past two years.
Similarly in Iraq, since the fall of Saddam Hussein in 2003, the Christian Iraqi population may have dropped by as much as 50%, according to a CIA assessment.
And despite making up only about 3% of the Iraqi population, Christians accounted for half the Iraqis who fled the country in 2010, about 200,000 people.
Egypt's religious tensions have a longer history than the recent clashes between Muslim Brotherhood supporters and Christians. Although then-President Hosni Mubarak kept a tight lid on the country's Islamist extremists, clashes between Muslims and Christians erupted sporadically throughout the '90s.
But since Mubarak's fall, extremist violence against Christians has picked up in Egypt. In early October 2011, Egypt saw its worst instance of sectarian violence in 60 years, when two-dozen Christians died in clashes with the military.
As a result of these kinds of attacks, by one estimate, around 100,000 Christians left Egypt in 2011.
This kind of homogenization has happened before in the Middle East, which boasted a sizable Jewish population in the '50s. But with the creation of the state of Israel and the rise of Arab nationalism and then Islamism, the region has become more hostile to non-Muslims.
Around World War II there were 100,000 Jews in Egypt, a community that had existed in Egypt since the time of the pharaohs.
Now, there are a handful of synagogues operating in Cairo. They are heavily guarded and generally empty as they cater only to the few dozen elderly Jews who are still left in Egypt.
One can only hope that this is not to be the fate of the Christians of the Middle East.
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