The pews at First Baptist Church of Bethlehem fill quickly as congregants stream in on a Sunday night, some with fancy purses, others with worn shoes and KFC takeout bags. Latecomers have to settle for plastic chairs in the back.

As the service gets under way, hands arc in the air as worshipers sing and thank God for a recent revival that drew more than 1,300 people to hear the message of the Bible – a testament to the theme of the sermon on this night: responding to the invitation of Christ.

In a city heralded as the place where Jesus Christ was born to the Virgin Mary, the church is something of a modern miracle. Founded in a two-bedroom apartment three decades ago by the Rev. Naim Khoury, First Baptist was bombed 14 times during the first intifada, struggled with financial difficulties, and is now facing a legal battle with the Palestinian Authority, which doesn't recognize it as a church.

Thousands of Christians in Bethlehem have faced similar political and economic strife over the past few decades, leading many of them to flee the city where Christianity's central figure was born in a straw-filled manger. Christians, who once made up 80 percent of the population, now represent 20 to 25 percent. But First Baptist defies the trend. Its congregation is 300 members strong – and growing.

"We fought and fought to remain and not to hide what we believe," says Mr. Khoury, who himself survived a bullet to the shoulder from an unknown sniper while in the church parking lot five years ago. "It's time for them to realize that we are here. There's no way for us to close down and go somewhere else.... We proved ourselves here by the help of the Lord that we are here to stay until the Lord comes back."

Khoury's unflinching faith is something that more Christians may have to summon – not only here in the Holy Land but across the entire Middle East. Two thousand years after the birth of Jesus, Christianity is under assault more than at any time in the past century, prompting some to speculate that one of the world's three great religions could vanish entirely from the region within a generation or two.

From Iraq, which has lost at least half of its Christians over the past decade, to Egypt, which saw the worst spate of anti-Christian violence in 700 years this summer, to Syria, where jihadists are killing Christians and burying them in mass graves, the followers of Jesus face violence and vitriol as well as declining churches and ecumenical divides. Christians now make up only 5 percent of the population of the Middle East, down from 20 percent a century ago. Many Arab Christians are upset that the West hasn't done more to help.

Though many Muslims grew up with Christian friends and colleagues, powerful political and social forces have made such coexistence more difficult. As political Islam gains support, Christians can no longer find refuge in a shared Arab identity with their Muslim neighbors, but are instead increasingly marooned by an emphasis on religious identity. Calls for citizenship with equal rights are punctuated with stories of Islamist extremists demanding that Christians convert to Islam or pay an exorbitant tax. And many Muslims are facing persecution themselves as the Arab upheavals of 2011 continue to ripple across the region and nations try to find an equilibrium between freedom and stability.

"Whatever happens, it is going to be very difficult to put it back together again," says Fiona McCallum, a scholar of Middle Eastern Christians at the University of St Andrews in Scotland.

To be sure, Christians have confronted difficult times before, from the killing of Jesus' immediate followers to the Mamluk oppression of Christians beginning in the 13th century to the rise of Islamist militant activity in Egypt in the 1970s. Warriors who came in the name of Christ have been responsible for egregious interreligious violence as well, such as during the First Crusade in 1099, when Christians took over Jerusalem and massacred nearly all the city's residents.

Whether today proves to be yet another ebb in the flow of Christian history or something more fundamental remains uncertain. But what is evident is that both Muslims and Christians, as well as the region's other minorities, are likely to be significantly affected by a continued deterioration.

Christians have traditionally run some of the region's top schools, been active members of the merchant class, and brought a moderating influence to society and politics. That has led not only Christians and human rights activists to lobby for the preservation of these communities, but some Muslim leaders as well.

"The protection of the rights of Christians is a duty rather than a favor," declared Jordan's King Abdullah in September, speaking to delegates at a palace-sponsored conference on Arab Christian persecution. "Christians have always played a key role in building our societies and defending our nations."

• • •

As an evening breeze sweeps across the Jordanian capital of Amman, dozens of Iraqi refugees file out of the Jesuit Fathers church, touching or kissing the cross on their way out.

Among them is Mofed, an Arab Christian who recently fled the turmoil in his native country. A year ago, Mofed (who, like other refugees, would only give his first name out of fear of retribution) was running a photo shop in Baghdad. Then one day several men came into his store and gave him three options: become Muslim; pay a $70,000 per capita tax (jizya) levied on non-Muslims; or be killed, along with his family.

"You pay, or get killed," says his wife, Nuhad. "There is no in between. If you say, 'OK, I'll become Muslim,' there is no problem. That is their aim, to get you to change your religion, to be Muslim."

Mofed and Nuhad decided to exercise a fourth option: flee their homeland, bringing their three children along with them. Their decision is emblematic of what an estimated half million Christians have done since the US-led invasion of Iraq in 2003 and the subsequent brutal civil war there. During that time, Muslim extremists have attacked more than 60 Christian churches across the country. This includes the 2010 Al Qaeda-linked strike on a mass at Our Lady of Salvation Church that killed 58 worshipers.

The proliferation of jihadist groups after the fall of Saddam Hussein, coupled with the rise of political Islam, has made an already tense environment even more unbearable for the country's Christian community, which has been part of Iraqi society for more than 1,900 years. While many Muslims have fled the turmoil in Iraq as well, Christians have been disproportionately represented, in part because of their above-average means: Four years into the war, Christians – who made up 5 percent of the population in prewar Iraq – accounted for 15 to 18 percent of registered Iraqi refugees in neighboring countries, according to the International Red Cross. Today, fewer than 500,000 Christians remain in Iraq from a prewar population of 1 million to 1.4 million.

Christians in Syria worry that the same thing could happen in their country, where civil war has led to a rise in militant groups, some affiliated with Al Qaeda. Many worshipers who once prided themselves on being part of one of the safest Christian communities in the Middle East now face kidnapping or death. Muslim militants are targeting Christian businesses as well. In recent months, jihadists have carried out assaults on the town of Maaloula, where many residents still speak Aramaic, the language of Jesus.

Athraa, a young Syrian mother, fled her village on the Syrian-Iraqi border with her husband and two boys to escape the dangers.

"We are expecting what has happened in Iraq to happen in Syria as well," she says, speaking in her modest Amman apartment, where suitcases teeter atop a run-down armoire.

Before the uprising broke out in March 2011, experts estimated that Christians represented 5 to 8 percent of Syria's 22 million people. The Syrian patriarch of the Melkite Greek Catholic Church recently suggested that as many as 450,000 of the 2 million Syrian refugees today are Christians, though such figures vary widely and are difficult to confirm.

While Iraq and Syria have seen perhaps the worst widespread violence against Christians, some of the most concentrated anti-Christian attacks this year have taken place in Egypt. That's of particular concern to Christians elsewhere in the region because Egypt's Christian population, at about 9 million, forms the largest Christian contingent anywhere in the Middle East. The church's demise there would be especially demoralizing.

Egypt's Christians, which make up about 10 percent of the population, face harsh restrictions on building or renovating churches, and say they often face discrimination in schools and the workplace. Violent attacks on Christians and their houses of worship rose in the final years of the rule of Hosni Mubarak, who was ousted in the January 2011 uprising.

As Islamists expanded their power after his fall, many Christians said the threat and attacks multiplied, particularly in the wake of Mohamed Morsi's election as president. But the violence didn't diminish once Mr. Morsi and the Muslim Brotherhood were removed from power this summer by the military. Many Islamists blamed Christians for supporting the coup, and angry Morsi supporters attacked dozens of churches across Egypt in August.

Samuel Tadros, author of "Motherland Lost: The Egyptian and Coptic Quest for Modernity," called it the worst spate of violence for Egypt's Copts since the 14th century.

It's not just Christians who are concerned. Sheikh Ali Gomaa, grand mufti emeritus of Egypt and one of four senior Muslim scholars to attend the Arab Christian conference in Amman this fall, condemned the attacks, church torchings, and humiliation of Christians in Egypt.

"This is a huge violation not only on the humanitarian level but on the Islamic level as well," he said. "It is incumbent upon us to eliminate this bitterness and tension, which is victimizing our brethren in Egypt."

Elsewhere in the Middle East, the situation is calmer but still difficult for many Christians. In Jordan, Christians make up 3 to 4 percent of the country's 6.3 million citizens but have a parliamentary quota of 6 percent and a government that promotes interfaith dialogue. In Lebanon, the Christian population remains the region's largest bloc in terms of percentage, with about 36 percent, and Christians are guaranteed half the seats in parliament by law.

In Gaza, fewer than 2,000 Christians remain. In a few cases, Christian church officials and family members have accused Muslims of forcing their relatives to convert to Islam – though the relatives themselves have said they willingly switched religions. (Editor's note: The original story didn't specify the source of the accusations of forced conversion.)

In the West Bank, Arab Christians are better off than many in parts of the region, but only an estimated 50,000 live there – about 2 percent of the population, down from 10 percent in 1920. Much of that change, however, is due to faster Muslim growth rather than an actual decrease in Christian totals.

One exception to the decline is Israel, where the Christian population has grown nearly fivefold, to 158,000, since the country's founding in 1948. Even so, their share of the population has dropped from about 3 percent to 2 percent, and critics note that Palestinian Christian families who fled or were forced out just prior to Israel's founding gave the country an artificially low baseline. Much of the increase was due to the immigration of Christians from the former Soviet Union, under Israel's expanded law of return, which welcomes those with a Jewish mother or maternal grandmother.

But there are also strong communities of Israeli Arab Christians – though they are not without their challenges. In Nazareth, for example, Islamists sought to build a mosque blocking the Church of the Annunciation. When thwarted by Israel, the Islamists settled for a banner proclaiming the Quranic verse: "And whoever seeks a religion other than Islam, it will never be accepted of him, and in the hereafter he will be one of the losers."

Michael Oren, who recently stepped down as Israel's ambassador to the United States, acknowledges that there is discrimination against Christians in Israel but says it's personal rather than official. "Compared to what's going on in our region, this is an oasis for Christians," says Mr. Oren. "The Middle East is hemorrhaging Christians, and no one is doing much about it."

• • •

Still, despite all the problems, this is not the darkest moment in history for Christians in the Middle East. Barbara Roggema, a scholar of Christian-Muslim relations at King's College London, notes that there have been many cycles of Christian persecution and prosperity over the centuries.

Under Islamic rulers such as the Mamluk sultanate of Egypt from 1250 to 1517, Christians – particularly those who had held government posts – were victimized by violence and discrimination. The subsequent Ottoman Empire granted Christians more autonomy and allowed them to flourish in many areas, though there were horrific exceptions such as the 1915 Armenian genocide that left at least 1 million dead.

Arab Christians played a key role in the Nahda, or Arab renaissance, of the 19th century, helping to propel the Middle East forward after centuries of deterioration under the Ottomans. Christians at the time embraced the idea of an Arab identity that was based on shared language and culture rather than religion, spearheading new schools and distinguishing themselves in literary circles. They also were highly successful traders.

But European colonialism complicated the dynamic, with some Muslims resenting what they saw as Westerners' preferential treatment of Christians. This fueled distrust and a perception that Christians are a Western import rather than an indigenous people – a stereotype that Arab Christians are still fighting today. The suspicions have only been exacerbated since the 2011 uprisings erupted across the Arab world.

Dr. Roggema sees three major differences between the problems Christians face today and those of the past: jihadist groups have access to arms on a scale unknown in history; propaganda can be more easily spread than ever before; and because of Western involvement in the Middle East, local Christian communities are more easily accused of being loyal to the West rather than to their own society.

"It is a gross historical and logical error to claim that being Christian equals being pro-Western, but it makes it easy for jihadists to accuse Middle Eastern Christians of not belonging to their own lands," she says.

Nasief Awwad was only 7 years old when his mother died, so his father – a Muslim laborer – decided to enroll him at a Mennonite-run boarding school in the West Bank city of Hebron. Later he transferred to the Hope Secondary School near Bethlehem, thus receiving not only the majority of his education but also much of his parenting from Christians.

Today, Mr. Awwad is the head of a major highway construction firm and serves on many local boards. At one point, he offered as many as 20 university scholarships annually for outstanding students. He credits his Christian schooling as a foundation stone of his success and says he enjoys correcting misconceptions about Christianity among his fellow Muslims.

"I appreciate all my life ... the help that I was given, the education that I got from the Mennonite school, from the Mennonite family – teachers and [the sponsors abroad] who paid for my education," says Awwad, who sent all four of his children to the Quaker-run Friends School in Ramallah. "I don't forget it."

The dividends of Awwad's Christian education underscore why many say it's important to maintain Christian communities in the Middle East. They see the quality of their schools; their contributions as entrepreneurs, merchants, and as overwhelmingly middle- or upper-class consumers; and the religious plurality they inevitably bring as essential and enriching to Arab society. Now, as their communities shrink or become increasingly marginalized, a key question is whether such positive influences will also dwindle.

In a way, the West Bank gives some sense of what other Arab societies might look like if Christian emigration continues. In Bethlehem, for example, Christian business owners once made up about a third of the stone and marble industry, while today they account for only 2 percent, says economist Samir Hazboun, who chairs the Bethlehem Chamber of Commerce. In the textile industry, they once owned about 80 percent of businesses, but the vast majority of those have closed.

They are doing better in the tourism industry. Today, 40 of Bethlehem's 43 hotels are owned by Christians, although they are rarely full, and many souvenir shop owners also say they're struggling. The economic challenges, often blamed on the Israeli occupation, have caused many Christians – as well as Muslims – to leave.

Some say the high quality of education offered by Christian schools unwittingly contributed to the Christian exodus – and with it the loss of an educated elite.

"The Christian schools that helped to educate Christians in the Gaza Strip and in the West Bank indirectly, without intending to do it, have encouraged the diaspora of the Christians ... and they did that through giving quality education to Christians," says Alex Awad of the Bethlehem Bible College, citing the broader horizons, European languages, and cultural familiarity that helped them to fit into Western societies. "It was a blessing to these individuals, but it hurt the community as a whole."

But those Christians who are left are active in society. According to the Lutheran-based Diyar Consortium in Bethlehem, nearly half of Palestinian civil institutions are Christian, and Christian institutions (including churches) are one of the largest employers after the Palestinian Authority, providing jobs for 22,000 Christians and Muslims.

"You will see that Christians have very important organizations, foundations, schools, hospitals. They lead very important and prosperous development in the city," says Mayor Vera Baboun, who says she and her fellow Christians also retain significant influence in the Palestinian Authority, with some serving as ambassadors and government ministers. "We are part and parcel of the decisionmaking process in Palestine."

To the extent such interactions are lost – or minimized by the persecution, segregation, or absence of Christians – experts believe it will be detrimental to society. "The narrowing of beliefs is already happening," says Nina Shea, coauthor of "Persecuted: The Global Assault on Christians." "There's intolerance toward the religious 'other' and that will continue.... Even when all the non-Muslims have been driven out, this drive for conformity will continue, and sects will turn on each other."

• • •

Amid all the persecution and violence, many Christians in the Middle East are able to survive by holding to two things – their faith and their fellowship with other Christians. Hany Sedhom, for one, has felt the support in concrete ways.

In late September, Mr. Sedhom, a husky, middle-aged Christian from the Egyptian city of Minya, was kidnapped, beaten, deprived of food and water, and threatened with death while the abductors urged his family to raise £300,000 (Egyptian; US$43,000) as a ransom. With the help of church members and Christian friends, his family was able to pay.

"The church acted as the body of Jesus. They were all praying for me," says Sedhom, recounting how, when he returned home after two harrowing days, members of his church and a religious organization he belongs to were waiting at his house with his family to welcome him. "These were the two things that made me survive – the hand of God and the church."

Sedhom is one of more than 80 Christians who have been kidnapped in the city of Minya alone since the 2011 uprising, with dozens targeted elsewhere in Egypt. They are kidnapped not for religious reasons, but because they are in a weaker societal position as a minority. They do not have families who retaliate like many Muslims do. And their close communities mean kidnappers expect they can raise large ransoms.

Other communities have seen more overt attacks on their faith, such as the St. Mina Church in Imbaba, which was attacked several months after Mr. Mubarak's ouster. But even here, church leaders urge congregants to deal with the threat by, in effect, turning the other cheek.

Head priest Abanoub Gad opens a worn Bible, some passages highlighted in bright pink, to Matthew 5:44, where Jesus told his disciples, "Love your enemies and pray for those who persecute you." Father Gad encourages his congregation to practice that teaching in their own lives and reminds them of the good relations they enjoyed with their Muslim neighbors and friends for decades, to emphasize that the extremists who attack churches do not represent the majority. While some clerics instructed Muslims not to offer greetings to Christians for Christian holidays, Gad says he told his congregation: "Go celebrate their feasts with them."

Many Christians believe that the centrality of forgiveness in Jesus' teachings could, in fact, play a vital role in helping to reduce sectarian violence across the Middle East.

"Christianity can bring a role model, a founder – Jesus, and his immediate disciples – who were not warriors, who were not trying to establish political power," says Paul Wright, an ordained Baptist minister, biblical scholar, and president of Jerusalem University College.

Khoury, from the First Baptist Church in Bethlehem, would certainly echo that sentiment. He encourages his flock to smile at the Israeli soldiers who staff the checkpoints around Bethlehem and speak kindly to them.

"I think the whole world is hungering and thirsting for someone to love them," especially in the Middle East, says Khoury. "Whatever it is, accept it, pray for them, forgive them, don't hold anything in your heart against them."

Ultimately, many argue, that is the kind of faith lived that will keep Christianity vibrant in the Holy Land and beyond. It is an approach that hinges more on the quality and fidelity of their faith than on the number of adherents – not unlike the early Christians who started out as a tiny, persecuted minority 2,000 years ago.

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"Unless [Christians] have ... spiritual and moral incentives, then whether they stay here or not, it doesn't make a difference," says Professor Awad of Bethlehem Bible College. "I think we have an understanding of God through Jesus Christ that can bless the rest of the population and help the Arab world with the struggles that they are having."

• Correspondent Kristen Chick contributed to this report from Cairo and Minya, Egypt.