Every day, Eddie Lyle gets fresh reports, e-mails and phone calls about a group of people who are now among the most persecuted in the world. It’s his job to bear witness to their story and, where he can, to visit them or to send one of his 35 staff to offer aid and comfort, and to lobby governments on their behalf.

His work has great impact, yet he speaks with little emotion. Those he campaigns for don’t usually elicit much sympathy.

“One of the world injustices least noticed in the West is the growing scale of Christian persecution,” says Lyle, who runs the British arm of Open Doors, a charity that works with afflicted churches and individuals. “We estimate that 200m Christians in more than 60 countries face the most brutal retribution because of their faith.” Christians have been persecuted, and have persecuted others, of course, since the Romans. What is unparalleled today is the sheer scope across the world. Take Bhutan: a Buddhist country with a religion usually associated with tolerance, it refuses to acknowledge that Christianity exists and is among the top 10 on the Open Doors 2007 list of global offenders.

The tradition of tolerance is under strain in India, too, from Hindu zealots. Anti-conversion laws aimed at evangelising have been passed in four states. For generations, many Christians were taught to pray for the conversion of communist Russia. Though the break-up of the Soviet Union restored the Orthodox Church to the heart of Russia, as Polish Catholicism helped to unravel the Soviet bloc, in some of the newly independent republics, notably Turkmenistan, Uzbekistan and Tajikistan, it has brought renewed persecution. Elsewhere, surviving communist states are continuing to repress. More Christians are imprisoned in China than anywhere else, a measure of the explosive success of underground or house churches. They may have as many as 70m members, vulnerable to arrest for non-regulated worship. In terms of severity, communist North Korea tops the Open Doors list, and International Christian Concern’s new “Hall of Shame”. Its capital, Pyongyang, was once known as “the Jerusalem of the East”. At least 50,000 Christians are now held in labour camps. Torture is frequently reported.

But it is across the Muslim world that persecution – sometimes government-inspired, but more often at mosque and street level – is spreading fastest. The problem is becoming acute along the fault line where largely Christian or animist Africa meets the Islamic north, from northeast Kenya and Ethiopia and Sudan, across northern Uganda and on into Nigeria.

Most startling of all is the ongoing Christian exodus from the Middle East. Once self-sustaining Christian communities have shrunk to the point where they may collapse. They are among the oldest in the world, for the region was the birthplace of the faith. Some have survived for almost 2,000 years. They predate Islam by six centuries. At the beginning of the 20th century, they still accounted for a fifth of the population. Fifty years from now, most may have vanished.

So serious is the exodus that Pope Benedict XVI recently called for Christians in the Middle East to avoid the “temptation to emigrate”. He spoke of his “deep concern” that they have to live with “little light and too much shadow”. Dr Rowan Williams, the archbishop of Canterbury, gave a stark warning when he was in Bethlehem last Christmas. “The first Christian believers were Middle Easterners,” he said. “It’s a very sobering thought that we might live to see the last native Christians in the region.”

Bethlehem, the town of Christ’s birth, is a case in point. It was 85% Christian in 1948. Today, that has fallen to 12%. Those who remain talk of themselves as “melting away”.

There are 80-year-olds in Jerusalem, city of 600 churches, who were born when more than half of the people in the Old City were Christian. Today, they account for barely 1 in 40.

Factors subtler than governments are often at work. In Egypt, the great bellwether of Middle East faith and intellect, Christians look to be thriving. They are the largest Christian minority in the Muslim world, about 10m strong.

Towards dusk on Thursdays, great numbers of children and their parents congregate at a rocky ridge overlooking Cairo. Several cave churches have been fashioned here from quarries and the living rock. The largest is a vast natural amphitheatre, the Virgin Mary and St Simon the Tanner Cathedral. Rows of seats cascade down to a cavern with an altar, with microphones and speakers for the choir. As the spotlights go on in the dying light, it hovers brilliantly above the city.

Below are the lanes and tenements and dumps of the city’s refuse-collectors. The rubbish comes in piled on donkey carts and trucks. It is picked through by hand, by families. The food waste goes to pigs that root through the yards, a sure sign that Cairo’s rubbish-recyclers are Christians.

Their children climb up the slope in their hundreds to the churches. Parents sip tea and crack jokes with the Polish sculptor in a hard hat who is here every day, devoting his life to the biblical scenes he is carving into the rock faces. Some take their toddlers to a small booth, to be tattooed with the cross on the inside of the wrist.

A young crowd, too, mainly teenagers, spills out of an evangelical church in central Cairo for a get-together on Tuesday evenings. “There’s a wonderful enthusiasm among these youngsters,” says the evangelical pastor. “The church is part of their life. Spiritually they are at home here.”

The monasteries, moribund in Europe, are coming back to life. The earliest monks and hermits were Egyptian. Wadi al-Natrum, off the highway from Cairo to Alexandria, had 50 monasteries and more than 5,000 monks by AD390, two centuries before St Augustine arrived in Kent. Four remain.

One of them, St Macarius, was on the edge of oblivion in 1970, surrounded by desert, and down to six monks. It now has 130, and 700 workers to tend the farms of its 2,000 hectares of land. Hermits come in from their caves in the desert once a week, for communion and to collect rations of bread, olives and cheese. “We work, and we pray, and we stay here until we die,” says Father Cedra. “We have left our family, our friends, our jobs.” The austerity appeals. “We can’t accept all the novices who come forward now,” he says. “There are too many.”

Most Christians are Orthodox Copts, but Anglicans figure among the other sects, small in numbers, their rivals say jealously, but rich in funds and buildings from the imperial past. One Wednesday last month, a service was held at All Saints’ Cathedral in Cairo for the investiture of Dr Mouneer Anis, already Bishop of Egypt with North Africa and the Horn of Africa, as Bishop of Jerusalem and the Middle East. The Grand Mufti of Egypt and the personal representative of President Mubarak were present.

At the studios of Aghapy TV, a Coptic Orthodox satellite channel, Bishop Botros is eloquent on the advantages that publicity has brought. It opened two months after a church in Alexandria was burnt in rioting.

“We have not had any big problems with the state since the channel started,” he says. “In the old days, nothing was published about what was going on. We were given just one hour on television, at Easter. With satellite, everything that happens inside gets known outside. Our trend is to be positive. Lots of young people are coming into the priesthood, many of them graduates, with PhDs, master’s degrees.”

In all these reassuring scenes, though, there is an edge of foreboding.

The tattooed crosses are an incitement to extreme Islamists. Within the church buildings, the evangelical youngsters are free to do and say what they want. “But outside the confines – no,” the pastor says. “Officials don’t want the common people to be upset.” The grounds of the Anglican cathedral are home to hundreds of mostly Christian refugees. Many of them are women. The cathedral has its own clinic. “We are dealing with 600 pregnant women a year,” says Dr Anis.

They have fled from Sudan and Darfur, Somalia, Eritrea, Djibouti, Ethiopia. Nobody is fleeing Egypt. But Christians are leaving, by the hundred thousand. Religious statistics in the Middle East are so sensitive that no census has been held in Lebanon for 74 years. Nobody knows how many Christians are in Egypt; 10m is a mid-range guesstimate. But everyone knows, for certain, that each year there are fewer.

Several factors are at work. The Muslims’ birth rate is higher, so that numbers tip steadily in their favour. Many Copts are highly educated, doctors, engineers, lawyers, and thus able to get work permits and settle in the West. Because the emigration is so long-standing, many already have family in the West.

So it is easier for Arab Christians to emigrate. These links in turn strengthen the feeling in the “Arab street” that those who stay are tainted by their contact with “crusaders” and “infidels”.

Hassan E is an embibi, a “Muslim background believer”, vulnerable as a convert to Christianity from Islam. “The fundamentalists are invading society in an increasing way,” he says. “The government has turned on them, but you find them everywhere: in charities, in state printing houses, in the security forces. Our society is being Islamised from the bottom up. The government owns authority, but fundamentalists own the people.”

“As Christians, we are big enough to be an irritant, but not big enough to really count,” says the evangelical pastor. “The system is designed to make you feel insignificant. It’s as if you’re living under a very low ceiling. Of course, there are many deep friendships between Christians and Muslims. But fewer among the young. There’s a sort of creeping segregation.” He says that there is a “green line” between the communities in Cairo, as there was in Beirut, where a literal green wilderness of destroyed buildings and gardens separated Christian from Muslim.

“Most civilised people respect this line,” he says. “They adapt. They are polite to each other. At street level, though, it’s different. If a Muslim knows a Christian, he’ll apologise for it: ‘My mechanic’s great, but I’m afraid he’s a Christian.’ ”

It is easy to get a neighbourhood to boycott a Christian grocer. “You just say, ‘He sells pork.’ We helped a widow set up a grocer’s after her husband died. The head of the local mosque said he would marry her, give her money for her children, if she became a Muslim. She refused.

“He pressured the landlord to throw her out. We put her in a new shop. They came and warned her to move, and then they set the shop on fire. Things like that happen all the time.”

The communities in Egypt remain viable. So are those in Lebanon, though civil war and last year’s Israeli incursion saw a million leave; Christians have long since ceased to be a majority.

A thriving community of 15,000 lived until recently at Antioch, now Antakya in Turkey, a city that has had Christians since St Peter preached there. They are down to a “handful” now. So few are left in Turkey as a whole that the Orthodox patriarchate in Istanbul may collapse for a shortage of candidates for the priesthood. The Iraqi invasion has been devastating for Iraqi Christians. The Commission on International Religious Freedom (CIRF), an official US watchdog, has warned that the exodus “may mean the end of the presence in Iraq of ancient Christian communities that have lived on these same lands for 2,000 years”.

In the early 1980s, there were about 1.4m Christians. Most were Chaldeans, Oriental Rite Catholics, or Assyrians. Many still spoke Aramaic-Syriac, the language of Christ. They were free to worship under the secular rule of Saddam Hussein. They kept a low profile – Tariq Aziz, Saddam’s foreign minister, was an exception to the Christian rule of avoiding politics – and were relatively prosperous.

Emigration was already under way after the first Gulf war. After the invasion, a co-ordinated attack by insurgent suicide bombers on five churches in Baghdad and Mosul in 2004 turned it into a flood. Within days, 40,000 fled to Damascus and Aleppo; thousands more sought sanctuary in the Kurdish north and Jordan.

Caught in the Shi’ite-Sunni violence, suspected by both of collaborating with the American “crusaders”, the Christians have no militia of their own to protect them. Police in Dora, a suburb popular with Christians in south Baghdad, say that at least 70% have gone. This followed kidnappings, bombings and demands by gunmen that Christians leave or pay jizya, the tax once imposed on non-Muslims over a century ago. Churches are burnt out or empty.

In Iran, President Mahmoud Ahmadinejad vowed in November 2005 to “stop Christianity in this country”. As in China, though, converts have increased despite a quarter-century of incessant anti-western and anti-Christian propaganda. They were put at 500, at most, before the Islamic revolution. They now number up to 20,000, joining the 200,000 ethnic Christians who have not emigrated.

The government of Saudi Arabia, the guardian of Islam’s holy places, is nakedly repressive. Religious police ensure that no Christian worship takes place in public, that no Christian preaches to a Muslim and that no Christian brings literature into the country. Saudi is classified by the CIRF as a Country of Particular Concern, but criticism is muted by western dependence on Saudi oil.

Outside the Arab world, Muslim-Christian tension is acute in northern Nigeria. At least 70 were killed and a dozen churches burnt after the Danish cartoons last year. Riots are sparked by the flimsiest “insult”. Twenty were killed, and two churches destroyed, after a teacher confiscated a Koran that a student was reading during her lesson. Islamic extremists in Ethiopia, one of the world’s oldest Christian countries, see it as a key to expanding in other parts of Africa. Jihad training centres – as many as 20, according to reports – have been financed by Saudi money together with Koranic schools to spread radical Islam. A campaign to convert Christians in Jimma last September led to a dozen deaths, with 850 houses burnt and 1,500 forcibly converted.

What can be done? A deep irony attaches to the lack of any firm British – or European – response, outside the specialist charities and the churches, though the latter have forged no united response. Persecution is often triggered by hostility to the West. To many, “the West” is synonymous with “Christian” – Arab Islamists often refer to it as “Rome” and to British and American troops as “crusaders” – and local believers are seen as its spies and stooges.

“Fundamentalists are very bitter and angry, because they are so severely repressed,” says an evangelical pastor in Egypt. “They rationalise it that Muslim governments repress them because of pressure from the West, and from Christians and Jews.” The same is true in Pakistan.

“There is a big confusion that the West is Christian,” says Dr Mouneer Anis, the Anglican bishop of Cairo. “We keep telling people that the West is secular, that its policies are secular, that the church is more and more being pushed away. They are not convinced.”

The result is that local Christians are blamed for events ranging from the invasion of Iraq to the Danish newspaper cartoons, over which they have no control. Satellite television and the internet spread news and religious incitement – Hamas TV channels, for example, eulogise suicide bombers – to places where happenings in Copenhagen once remained unknown. “We are always linked with the West, but the West doesn’t recognise us,” says Nasir Saeed, the UK co-ordinator of Claas, which gives legal aid and support to Pakistan’s 3m or so Christians. “If any western country acts against Muslims, fundamentalists persecute Christians in Pakistan. Our churches and houses are burnt; we are attacked and sometimes killed. People seem not to realise the price we are paying.”

That is not true of the United States. The CIRF was specifically set up in 1998 to monitor religious repression. It sends its reports, listing Countries of Particular Concern, to Condoleezza Rice at the State Department. American pressure is widely applied and has been decisive in several individual cases.

In Britain, where Rowan Williams says God “is excluded from the human conscience”, and Europe, which the Pope says is now “Godless”, indifference and ignorance reign. Sympathy for “fellow Christians” has evaporated in societies that have ceased to practise their traditional faith. There is little will to protect Christians in other countries, and widespread ignorance of the churches and cultures of eastern Christendom, of Christian traditions in Alexandria, Baghdad, Constantinople. But the grassroots cause for the lack of response is what Dr Michael Nazir-Ali, the Bishop of Rochester, calls the “chilling spiritual vacuum” in Britain. A once proudly Christian country has become “inaccessible” to the church. “It struck me at the moment in Diana’s funeral when the archbishop led the congregation in The Lord’s Prayer,” he says. “The cameras went to the masses of people outside. They could start it. But they couldn’t get beyond the second line.” Pakistani-born, he has a special interest in the fate of far-flung communities. “Persecution is getting worse,” he says. “It’s not simply Muslims. Secularists in Turkey are very hostile. I have met a Chinese Pentecostal who has been arrested 26 times. The last time, she was beaten so badly she told me she wanted to die.”

The large Pakistani community in Britain gives the situation there particular resonance. Discrimination and assaults against Christians and other minorities continue apace. The main engines of repression are the blasphemy laws and the Shariat Act passed in 1991, which makes Islamic sharia the “supreme law”. Sharia is Islamic law based on the injunctions of the religion, but no universally accepted codification of these injunctions exists.

Amnesty International complains that the blasphemy laws have been “consistently used to harass, intimidate and detain” minorities. They are used to settle grudges and as blackmail. Bishop John Joseph, the Catholic Bishop of Faisalabad, shot himself in 1998 in protest. “Our people try to live normally, but are afraid of being accused,” he said shortly before his death. “This is becoming a terrifying psychosis.” He was distraught over the case of a member of his congregation who was condemned to death for allegedly praising Salman Rushdie’s The Satanic Verses. The charges were intended to force Christian families to acquiesce in a land dispute.

The Hudood Ordinances on rape and adultery, says Nasir Saeed of Claas, left Christian women vulnerable to being “abducted, raped and forcibly converted to Islam”. The need to produce four male adult Muslims as eyewitnesses made it almost impossible for a non-Muslim woman to prove rape. Non-Muslim witnesses were not admissible in cases against Muslim men. The evidence of two women counted as that of one man, and the presiding officer of the court had to be Muslim. The ordinances are being amended, but Saeed says much damage has been done.

Christians cannot vote as part of the general electorate, but only for Christian candidates for the four parliamentary seats allocated to them. Muslims graduating in higher education are given an additional 20 marks for hafiz-e-Koran, knowing the Koran off by heart. This is a source of considerable bitterness, since Christians have contributed greatly to education in Pakistan. Both the present president and prime minister attended Christian-founded schools.

Attacks on Christians, though roundly condemned by President Pervez Musharraf, have become a constant backdrop. The worst incident was in Bahawalpur in October 2001. Masked gunmen burst into St Dominic’s Church during a service and killed 16 people, including children.

Those immediately concerned differ in their response. Copts are diplomatic and keep within themselves. “The Coptic Church is like a great fortress where they are protected,” says an evangelical. “They don’t approve of us, because we want to reach out – it’s part of our DNA – and that can cause them problems.”

Anglicans also feel great care should be taken with protest. “We should differentiate between ‘incidental hardship’ and ‘persecution’,” says Dr Anis in Cairo. “If we say ‘persecution’, people think it’s government policy. It isn’t.”

Rowan Williams holds the British government in part responsible. He said that its “short-sighted” policy in Iraq has put Christian communities at risk across the Middle East.

At the same time, the start of real problems in the region can be dated back at least to the foundation of Israel in 1948. Iraq has only made an existing problem worse, some say privately, and blaming the West lets Israelis, corrupt regimes and fundamentalists off the hook.

“Why do people in the West always apologise?” asks a young Presbyterian pastor in Cairo. “I listen to the BBC, and they are always reporting that England has a history of occupation and guilt. Why do European leaders all want to say, ‘We love you’? Fundamentalists are evil. We are a minority. We live under their nose. We aren’t afraid. Why are you, in a free country?”

The Pakistani Muslim community in Britain, Nasir Saeed says, should look at the privileges it enjoys here. “Those freedoms are denied to Christians in Pakistan,” he says. “We have always prayed for the wellbeing of the country. But we are seen always as inferiors, as spies linked to the West. They are the first to take offence. But they expect us to live under constant duress.”

Communism may well wither on the vine in Asia, as it has in Europe, while religious regimes grow. “Islamisation, of one sort or another, is the biggest challenge,” says Dr Nazir Ali. “All over Europe, there is proselytising. There’s nothing intrinsically wrong with that. But it’s the extremists, violent sectarians, who are doing it.”

It is not going to go away. Charities cannot deal with its effects single-handedly. Society will have to come to terms with it. The bishop warns that it will be a long haul. “Religion is still a part of the identity of the outside world in a way the West no longer recognises,” he says. “We have forgotten the part it played in our lives.”

It may seem bizarre for Eddie Lyle to serve foreign Christians from a Britain whose national airline tried to ban staff from wearing the crucifix, and a Europe whose parliament blocked Rocco Buttiglione from becoming EU justice commissioner because of his Catholic beliefs.

“I’m just back from Indonesia,” Lyle says.

“I was visiting three ladies who suffered terribly for what the authorities called child abuse. You and I would call it running a Sunday school. Persecution has always deepened Christian faith. It’s wonderful to see that it still does.”

Open Doors is at www.opendoorsuk.org ; Claas is at www.cltf.org.uk