What Liberation

Punctuation available on request. Edward Stourton writes:

Fr Rayan Paulos Atto showed me an elaborately decorated bronze and glass case mounted on the wall near the altar of his airy modern church in Erbil. It was a reliquary, a showcase for displaying a relic of a saint or martyr – the sort of thing you might find gathering dust in the sacristy of some venerable Italian basilica.

Fr Rayan's reliquary contains a miniature icon of the Virgin which is spattered with tiny droplets of blood – the blood of his closest friend, a priest gunned down on the steps of his church in the name of Islam. For Christians in Iraq today the possibility of martyrdom is an ever present reality, not a historical curiosity.

The campaign of violence against Christians is one of the most under-reported stories of Iraq since the invasion of 2003. And it could change the country's character in a fundamental way; by the time the dust finally settles on the chaotic current chapter of Iraq's history, the Christian community may have disappeared altogether – after 2,000 years as a significant presence. About 200,000 Iraqi Christians have already fled the country; they once made up three per cent of its population, and they now account for half of its refugees.

Erbil, in northern Iraq, has become a magnet for Christian refugees who are too poor to leave Iraq or do not want to abandon their country. It is the seat of the Kurdish Regional Government, which treats the Christians well; it is safe; and there is an established Christian community to welcome them. Many of them gravitate towards the traditionally Christian suburb of Ainkawa.

Ainkawa is a 15-minute drive from the centre of Erbil, and on the way there, with Fr Rayan at the wheel, we passed the motorway exit to Mosul. Mosul – the biblical city of Nineveh – is only 50 miles from Erbil, but it remains a fearsomely violent place and it was there that Fr Rayan's friend lost his life.

The two of them had met in Rome, where they were both studying theology. Fr Ragheed Ganni, who was a little older, showed him the Roman ropes, and they formed a close bond that endured when they returned to parishes in Iraq.

Fr Ragheed began to receive threatening letters from Muslim extremists telling him to close down his church, but he refused to do so. The gunmen simply turned up at the end of mass one Sunday and shot him, together with three of his sub-deacons. I asked Fr Rayan whether he would be willing to take on a job in Mosul now. "Sure, why not?" he replied in measured tones. "I would do it. I think being a martyr is something very special".

Almost every day refugee families turn up from Mosul or Baghdad asking for Fr Rayan's help in starting a new life. And with them they bring stories of the continuing horror they have left behind. The latest trend in Mosul is young men and women being stopped on the street and asked for their identity cards – and shot if their names reveal their Christian origins. "They used to ask for money first," Fr Rayan said. "Now they just kill them right away."

Ainkawa quickly reveals itself as a Christian neighbourhood; beer, spirits and white wedding dresses are displayed in the shop windows along the main street. The suburb has grown like Topsy since it became a haven for Christian refugees; Fr Rayan grew up here and can remember the days when it was little more than a farming village. About 1,000 families lived in Ainkawa at the time of the invasion; since then the number has increased six-fold.

New housing is being thrown up all over the place to accommodate the influx. Many of the streets where refugees have been settling are scruffy, half-built developments on the outskirts. Families who have left prosperous businesses and comfortable homes behind in Baghdad have opened jerry-built convenience stores to serve their neighbours.

A woman running a vegetable stall told me that she and her husband left Baghdad after 36 years when their church was bombed. She went back recently to investigate whether she was entitled to a food allowance from the government, but fled again because a group of young men knocked on the car window and threatened her for not wearing a headscarf. A family in the neighbouring street said they had fled Baghdad after their nephew was shot dead as he left church after a prayer meeting. A middle-aged man explained stoically that his son had been kidnapped and never heard of again. "He would have been 25 now," he said. "It would be very expensive to find out what happened to him, and I don't have any money." His second son is in the United States.

Fr Rayan took me to Ainkawa's oldest church, St George's. It has a cool, whitewashed interior, and its domes are supported on massively thick pillars. No one knows quite how old it is; there is a stone with an inscription recording the rebuilding of the church in the seventh century, but Fr Rayan believes the first church on the site was established in the third or fourth century. It would have been a centre of Christian life long before St Augustine turned up in Canterbury, and probably pre-dates the birth of the Prophet Mohammed by several centuries.

The antiquity of Iraqi Christianity was brought home to me during Vespers at St Joseph's, a big new church in the centre of Ainkawa. The prayers were in Aramaic, the language that Jesus would have spoken.

Church tradition holds that Christianity was brought to Jewish communities here by the apostles Thomas and Thaddeus, and it is certainly plausible that Christianity put down its first roots in the area while St Paul was on his early evangelising journeys to Greece and Rome. There is good historical evidence that Christianity had established itself in what was then Mesopotamia by the early second century.

Christianity's fortunes under Islam were mixed. There were periods in the early centuries of Arab rule when Christian scholars and doctors played an influential part in the life of the Abbasid caliphate, and a ninth-century patriarch writes of monks being despatched from what is now Iraq to evangelise in China and India.

Christians were persecuted and sometimes massacred during the turbulent period that lasted from the late 13th century until the early 16th century, and were forced to live as second-class citizens under the Ottomans. But Christian communities survived, and even under Saddam Hussein their place in Iraqi society was secure: his notorious foreign minister, Tariq Aziz, was a Christian, and in Ainkawa there is a memorial to the Christian young men who died in Saddam's war against Iran.

Little of this rich history is widely known in the West. The Archbishop of Canterbury, Rowan Williams, is a passionate advocate on behalf of the region's Christians. "The level of ignorance about Middle-Eastern Christianity in the West is very, very high", he said. "A good many people think the only Christians in the Middle East are converts or missionaries. I have heard some quite highly placed people, who ought to know better, saying that."

I asked Dr Williams about the two politicians who took us to war in Iraq: Tony Blair and George Bush were the most enthusiastically Christian leaders we have had for many years. "The Christianity both of them were shaped by is, on the whole, a very, very Western thing," he said. "I don't sense that either of them had very much sense of the indigenous Christian life and history that there is in the region."

Iraq's Christians blame Western ignorance for many of their problems. Louis Sako is the Chaldean Archbishop of the Northern Iraqi city of Kirkuk: the Chaldeans are the largest of Iraq's Christian denominations. He is scathing about the Western missionaries he says came piling into Iraq in the immediate aftermath of the American invasion looking for converts.

In Baghdad alone, he told me, 30 new churches opened up shop, "with money, with books they were handing out to people on the street. I think this is provoking people. A Muslim cannot change his religion. It is not allowed. And they think they are here as missionaries to gain Muslims for Christianity."

The Chaldeans are in communion with the Roman Catholic Church, and Louis Sako has been instrumental in persuading Pope Benedict to convene a special synod on the plight of Christians in the Middle East this October. In a pamphlet he has produced to bring the issue to the world's attention he writes: "Iraq is our homeland – we have been here long before the arrival of Islam. We are an indigenous people, not some colonial entity from somewhere else."

But he says that, since the invasion, many Iraqi Muslims have come to see Christians as exactly that – a colonial entity. Christianity has become associated with the West, and therefore with the Occupation.

The factors behind the eruption of violence against Christians are complex. Canon Andrew White, the redoubtable vicar of Baghdad, has watched the process from the start: he first came to the Iraqi capital in the late Nineties to reopen the city's one Anglican church, St George's, which had been closed down after the first Gulf War.

He, too, points a finger at western ignorance of Iraq's religious ecology. He recalls an early meeting with Jerry Bremer, the pro-consul sent by George Bush to sort out the chaos in Iraq in 2003. "I said we have to deal with the religious leaders and sectarian issues nowe_SLps Bremer said to me, 'Oh, don't worry about that. This isn't a religious country at all. It is very secular.' " It did not take long for Ambassador Bremer to change his mind. When they met again, he told Andrew White: "I can't even deal with water and electricity because religion keeps getting in the way."

Canon White has a weakness for loud bow-ties. He is a giant of a man and cuts an incongruous dash as he strides around the heavily fortified compound of St George's in his crisp blue blazer, a gun-toting Iraqi police officer seldom far from his side. "At the end of October, there was a major car bomb attack here," he remarked airily, "164 people were killed. And David [here he gestured at one of his Iraqi assistants] had to pick up all the arms and legs and hands and bits of body."

That bomb was probably aimed at a nearby government building rather than the church. One of the reasons Christians have suffered in Iraq is simply that they have been caught up in the general violence like everyone else. But another is certainly that, as a religious minority, they are especially vulnerable in a society that has fractured along sectarian religious lines.

Rowan Williams thinks the collapse of the historically good relations that Iraqi Christians enjoyed with their Muslim neighbours reflects a wider trend in the Middle East. "If you speak to a great many Muslims in the Middle East," he said, "you will hear them saying: 'Until a couple of decades ago, our version of Islam was one that was happy to co-exist, but we suddenly find heavily funded, very active, very aggressive, very primitive Islamic groups coming in and telling us that we have never really been Muslims at all, and re-shaping the whole of our relations with the rest of the community.' "

Andrew White knows what that trend means on the ground. Last year, he agreed to baptise 13 Iraqi Muslims who wanted to join his church. Within a week, 11 of them, he told me, had been killed.

I asked Rowan Williams whether he thought we might see Christianity disappear from the Middle East altogether in our lifetime. "I am sad to say that I think it is a possibility," he said, "and a possibility that appals me."

Edward Stourton presents Iraq's Forgotten Conflict on BBC Radio 4 on Tuesday at 8pm.