The war on Christianity: The religion's followers are dwindling in the land of its birth - and it's not a crisis of faith, but one of violence

Almost fifteen hundred years ago, a wandering monk called John Moschos described the Eastern Mediterranean as a "flowering meadow" of Christianity. The religion had been born here nearly 600 years before but while, in the early years, it had been a persecuted, militant cult, under the patronage of the Byzantine emperors it had matured and mellowed. "The meadows in spring present a particularly delightful prospect," Moschos wrote in his book The Spiritual Meadow, which became a 7th-century best-seller. "One part of this meadow blushes with roses; in other places lilies predominate; in another violets blaze out…"

Christianity, in other words, was now flourishing right across the region. No intolerant tyranny menaced it, no other religion contested its right to grow and prosper and develop in different ways. "The Eastern Mediterranean world was almost entirely Christian" in Moschos's day, William Dalrymple wrote in his 1997 book From the Holy Mountain. "At a time when Christianity had barely taken root in Britain… the Levant was the heartland of Christianity and the centre of Christian civilisation… The monasteries of Byzantium were fortresses whose libraries and scriptoria preserved classical learning, philosophy and medicine against the encroaching hordes of raiders and nomads [and] the Levant was still the richest, most populous and highly educated part of the Mediterranean world."

Today, the picture is dramatically different. Every corner of the Middle East is locked in more or less violent struggle, but whatever course the future takes, it is safe to predict that Christians will play only a marginal part in it – if they survive at all. Already, as the Prince of Wales recently pointed out, there is a smaller proportion of Christians in the region than in any other part of the world: just 4 per cent, and falling fast. Sunni Muslim extremists see them not as "people of the Book" – members, like Muslims, of one of the three great Abrahamic religions – but as infidels, bracketed as the odious Other alongside Shias, apostates, atheists, Baha'is.

For Muslim extremists, the Christian minority has become a favoured target because they belong to the "wrong" religion; are numerically few, weak and vulnerable; and are identified with the oppressive policies of the Christian United States and Europe.

As Dr Khataza Gondwe, of Christian Solidarity Worldwide, told me: "In Egypt and elsewhere, extreme Islamism portrays Christians as a non-legitimate or foreign community that has no right to be there – as a special interest group of the West. In Iraq, the debate surrounding the invasion and war has distorted the issue and, meanwhile, the Islamist extremists there have decimated one of the oldest Christian populations in the world."

Christians, of course, have no monopoly on persecution. According to the Pew Research Centre, the number of countries in which religious groups experience harassment or intimidation soared from 147 in mid-2009 to 166 in mid-2010; one-third of all countries experienced high levels of hostility involving religion, up from only one-fifth in 2007. In recent years, not only Christians but also Jews, Buddhists and followers of folk or traditional religions have all experienced persecution in more countries than ever before. In 2010, Christians were harassed in 111 countries, but Muslims were not far behind, abused in 90 countries, while Jews were harassed in 68 countries.

Social hostility involving religion is never a one-way street: the abuse of adherents of one religion often leads directly to attacks on the community from which the abuse came, either in that country or elsewhere. Seen from this perspective, the world seems locked in a downward spiral of religious intolerance and hatred. And Britain is not exempt: the Pew Research Centre found that the UK had the highest incidence in Europe of social hostility connected to religion, even worse than countries such as Burma, Uganda, Thailand and Algeria, where such hostility is endemic.

Some of the most shocking cases of religious persecution in recent years have involved Muslims. Twelve years ago, in the Indian state of Gujarat, nearly 800 Muslims died in riots orchestrated by Hindu nationalist militants. In Burma, violence against Muslims committed by Buddhists, including Buddhist monks, has erupted repeatedly since the killing of a Buddhist girl in Arakan state in June 2012, despite condemnation by the outside world.

But those ugly events are peculiar to the countries in which they occurred. The attacks on Christians, by contrast, follow a clear pattern from country to country. From Nigeria and Somalia via Egypt, Syria and Iraq to Pakistan, Christians are being targeted ever more frequently by Islamist extremists. A sample of atrocities across these countries gives an idea of the rising tide of terror from which Christians are suffering:

µ In Egypt, many supporters of deposed President Morsi irrationally blamed Coptic Christians for his downfall, and took revenge on them. They seized control of the remote town of Delga, burning down three of the five churches there, and forced thousands of Christians to flee. They looted the 1,600-year-old monastery of the Virgin Mary and St Abraam and set fire to it. "They [the Copts] alone were set up as scapegoats and erroneously blamed for instigating the violent dispersal of pro-Morsi demonstrators," Bishop Angaelos, of the Coptic Orthodox Church in the UK, told a US Congressional hearing.

µ In Syria, as jihadists gained the upper hand over more moderate rebels, the village of Maaloula, where many still speak ancient Aramaic, the language of the Bible, was invaded by rebels who attacked churches, forcing many among the 3,000-strong population to flee. Elsewhere in the country, two archbishops were abducted by gunmen in April last year and have yet to reappear.

µ In Iraq on Christmas Day, 24 people were killed when a bomb exploded outside a church in Doura, southern Baghdad, as worshippers were leaving at the end of a service. Dozens more Christians were killed elsewhere in the country during the Christmas period. Prior to the Iraq war, there were 1.4 million Christians in the country, around 3 per cent of the population. Since then, the number has fallen to about 300,000. Raphael I Sako, the Chaldean Patriarch of Baghdad, said: "If emigration continues, God forbid, there will be no more Christians in the Middle East. [The Church] will be no more than a distant memory."

µ In Pakistan, 85 Christians were killed when two suicide bombers blew themselves up outside a historic church in the frontier city of Peshawar in September 2013. Standing in the church's courtyard and comforting the wounded, the Bishop Emeritus of Peshawar, Mano Rumalshah, commented afterwards: "It's not safe for Christians in this country. Everyone is ignoring the danger to Christians in Muslim-majority countries. The European countries don't give a damn about us."

Christian campaigners have long lamented the reluctance of politicians or media in the West, and Europe in particular, to take a stand against the growing wave of violence. Dr Gondwe remarks that "sectarian attacks on Egyptian Copts have been occurring for decades, but many people in the West have appeared reluctant to speak out. For a time, it seemed as if journalists and human rights organisations were anxious not to be seen as displaying a bias towards Christianity."

But now, says Dr Gondwe, there has been "a complete turnaround. In Nigeria, the brutality of the Islamist militia Boko Haram has meant that people could not ignore the events on the ground. In Egypt, Copts and young Muslims participated alongside each other in the Tahrir Square protests, and members of the Muslim community speak out strongly against sectarian violence. There are voices in the Muslim community saying: 'We are Egyptians first'."

Meanwhile, the recent changes at the top of the Catholic and Anglican churches have also made a difference, with Pope Francis and Archbishop Welby focusing attention on persecuted Christians. But it was Prince Charles who said the previously unsayable in a blunt speech to religious leaders at Clarence House at Christmas. "We cannot ignore the fact," he told them, that [Christian communities in the Middle East] are increasingly being targeted by fundamentalist Islamist militants." He went on to except Jordan from the charge – "Jordan has set a wonderful example… [it] is a most heartening and courageous witness to the fruitful tolerance and respect between faith communities."

Yet the latest research – from Open Doors, a US organisation that publishes annual figures for Christian persecution – shows that jihadi violence is increasingly spilling over into Jordan from the Syrian civil war, causing Jordan to jump up eight places in the list of countries where Christians are most at risk of persecution.

The long period during which the persecution of Christians was downplayed in the West has clearly ended; now there is a risk of swinging too far the other way. An American research organisation, the Center for the Study of Global Christianity, has claimed that 100,000 Christians are "martyred" every year. But closer examination reveals that this figure includes the deaths of tens of thousands in war, in the Democratic Republic of Congo and elsewhere, whose faith was only an incidental factor in their deaths. As Judd Birdsall, formerly of the US State Department's Office of International Freedom, points out, this "expansive definition… doesn't ring true to the religious freedom activists who carefully monitor persecution and martyrdom year after year". Additionally, Birdsall says, it "risks cheapening" the meaning of martyrdom. His department produces estimates of Christian martyrs ranging from dozens to hundreds per year. Some Christian human-rights organisations place the figure higher, but no greater than 1,000.

What is beyond dispute, however, is that Christians are being deliberately killed in large numbers on account of their faith in the region where it first flourished. When John Moschos was gathering his "flowers" from the unmown meadow of Christianity in the late 6th century, the Byzantine Empire was already in steep decline, and it was not long before the followers of the Prophet Mohammed finished it off. Yet, despite the loss of its imperial protector, Christianity in the region has survived more than a millennium of Muslim domination. Its congregations may have shrunk and its culture stagnated, but it was permitted a place and a role of its own both in the Ottoman Empire and in the nation states that succeeded it.

The idea that Christians – those fellow People of the Book – should be bombed and slaughtered and terrified into flight, their churches and monasteries burned down and their history expunged: these evil developments are quite new. The Nazis did their best to wipe out all trace of Judaism in Europe. A similar effort – less systematic and scientific, certainly – now menaces the survival of Christianity where it was born. We are beginning to see this disaster for what it is. But it may be too late to reverse it.