Three members of his family had already been murdered before Shamon Isaac decided to leave Baghdad. First, his son-in-law Raid Khalil was shot dead in January 2005 as he fled gunmen who had tried to pull him and his father into a minibus. Like many Christians, Khalil had received a death threat signed by the Islamic Army in Iraq. He left behind a widow and a baby girl, who is now nearly two.

Four weeks after Khalil was killed, Isaac's brother was stopped at a checkpoint by seven men in Iraqi army uniforms as he was on his way to collect passports to take his own family out of the country. "People in the neighbourhood shouted to his daughter that her father had been assassinated," Isaac said, "and she came out and found his body in the street." Then last August Isaac's brother-in-law was shot dead in his shop by three gunmen.

Finally Isaac and his family had no choice. When in January this year cars started to circle the family home in al-Dora with men shooting in the air, they escaped to another Baghdad neighbourhood, al-Jediya. But major demonstrations were taking place throughout the Muslim world in response to the Danish cartoons and on January 29 bombs ripped through seven churches in Baghdad, Mosul and Kirkuk, killing 16. Then one day a man walked into the small shop that the family had just opened next to their new home, bought some cigarettes and walked out, but not before he had left a letter on the counter. On opening it, they found it contained a single word: "Blood."

The mechanisms of terror in the new Iraq have uprooted families from every community, including Sunni and Shia, Arab and Kurd. But although Christians made up less than four per cent of the population - fewer than one million people - they formed the largest groups of new refugees arriving in Jordan's capital Amman in the first quarter of 2006, according to an unpublished report by the UN High Commission for Refugees (UNHCR). In Syria, which has a longer border with Iraq, 44% of Iraqi asylum-seekers were recorded as Christian since UNHCR began registrations in December 2003, with new registrations hitting a high early this year. Fleeing killings, kidnappings and death threats, they come from Baghdad, from Basra in the zone of British control and, disproportionately, from Mosul in the north. The Catholic bishop of Baghdad, Andreos Abouna, was quoted recently as saying that half of all Iraqi Christians have fled the country since the 2003 US-led invasion.

Yet their exodus has gone largely unreported, despite the fact that both George Bush and Tony Blair have spoken about how their own Christian beliefs have informed their policies in Iraq. In one of his first speeches after 9/11, the US president described the fight against terrorism as a "crusade", a characterisation that he wisely dropped but which is habitually repeated by critics of US foreign policy, including al-Qaida and other insurgent groups in Iraq. Many Christians have been accused of association with the multinational force, or of supporting the west. Now Iraqi Christian leaders are bitter that the west has done so little to protect them.

When Isaac fled Baghdad with 11 of his family it was, naturally enough, to the ancient home of Iraqi Christianity that they came - to the plains of Nineveh. I met them there three weeks later, huddled in a room in Bartallah, outside Mosul, part of the great fertile flatland on the banks of the Tigris where nearly every village has its church, and each church now has an armed guard. The plains are among the longest continually habited places on earth. It was to save Nineveh that the Biblical God delivered up Jonah from the belly of the whale, and the Assyrian Christians here still speak Syriac, a dialect of Aramaic, the language Jesus Christ spoke with his apostles.

But Nineveh's unique place in Christian heritage counts for little today beside its strategic value in the geo-ethnic endgame of the Iraqi conflict. Situated between Iraqi Kurdistan and the insurgent strongholds west of Mosul, the Nineveh plains are central to the security of both, and to the territorial ambitions of Kurds and Sunni Arabs alike. Travelling in Iraq as part of a human rights mission coordinated by the charity Minority Rights Group International, in association with the UN Assistance Mission for Iraq (Unami), I was told that no aid workers had been able to operate here since May 2004, when four Americans from a Baptist charity were killed in an ambush on the Mosul-Erbil road.

In Mosul city, both the Ba'athists and the Islamist groups had deep bases of support that enabled them to control whole neighbourhoods and, periodically, the city's police. "They stopped a Christian woman from Mosul university, took her away and cut off her head," the manager of a women's welfare organisation told me, her face flushed with the imagining of it. "They said that if anyone comes to college without hijab, they will be killed."

"The poor security situation covers all communities in the city," explained Dr Yousef Lalo, the assistant governor of Mosul. "But as a minority, the Christians are particularly vulnerable. They are also often more affluent than other communities, so people try to extract money from them." A former psychology lecturer, Lalo's habitual companions are no longer students but the bodyguards that testify to his status as the only remaining Christian in the city's senior administration.

"Many churches were bombed in 2004 and 2005 but the multinational force and the Iraqi national army did not find out who was responsible; they didn't even do a proper investigation. It got worse and few people turned up even for Christmas and Easter celebrations. Now the Christians protect their own churches."

Lalo couldn't provide a number for how many Christians had left Mosul, but said that "thousands" had emigrated to Jordan, Syria and Turkey. "Half the Christians in Mosul have left since 2003 and the rest are planning to leave if they can. Many of my family have emigrated to Australia and Sweden and become refugees."

But this softly spoken professor was staying to fight. "This is my land, and the land of my father and grandfathers, and I will not leave. I have also forbidden my three sons to emigrate."

That morning, Lalo had his first meeting with the multinational force commander for Mosul and eastern Nineveh, Colonel Michael Shields. Although "meeting" is perhaps not quite the right word for an encounter that began when four US soldiers in full battle dress came through the front door unannounced, the commander demanding: "Who's the leader? Where's the leader?" But once the Americans had put down their weapons and body armour, the exchange that followed was polite enough. I knew Lalo was bitter that the US had supported the appointment of a Muslim mayor in a predominantly Christian area and Shields told me he was working hard to improve contacts with local officials. He explained: "Nineveh province is an ethnically challenging area. If the governor shows favouritism, that creates problems." Lalo ventured bluntly that Shields' predecessor had been "bad for the Christians". "That," the colonel said, "is water under the bridge."

The Christians' last hope in Iraq may just lie, according to Lalo, with Sarkis Aghajan, minister of finance in the Kurdistan regional government and, until last May, Kurdish deputy prime minister. It is he who has been channelling money to Nineveh to pay for armed guards.

In his palatial residence in Ankawa, a Christian neighbourhood in Iraqi Kurdistan, he talked about his community as he sat between a picture of the crucifixion and the statue of an eagle. "As Christians," he said in Syriac, "we regard Nineveh as our region. Throughout history our people have been obliged to leave and live elsewhere." This included those who had fled Saddam Hussein's campaign to "Arabise" Kurdish and Christian areas in the north, when land was redistributed by force to Arab settlers. But now, he explained, about 3,500 families had come from Mosul and Baghdad to settle in the Nineveh plains.

"More than 30 Christian villages have been restored. But people will not return unless they feel their national rights are protected. Before, people were kidnapped on a daily basis. We increased the number of armed guards and now there are thousands. We are not threatening any other party, but the Kurds look out for the Kurds, the Arabs for the Arabs, so we have to protect ourselves too."

But Aghajan's ambitions go further. He is convinced that the only way to secure protection in the longer term is for an autonomous region, a safe haven, to be established covering Nineveh's Christians, as well as smaller minority communities there such as the Yezidis and the Shabak. "This special region would help us to maintain Christian history in that place. In that way, there would be no way for Kurds or Arabs to intervene. This would encourage the Christians living outside to come back, and it would be an example in the Middle East."

Aghajan is also sure that such an autonomous region should be part of an enlarged Kurdistan, prompting some politicians from Nineveh to accuse him of serving a Kurdish agenda. One, who fears the prospect of Kurdish control as much as a return by the Ba'athists, described him as "prime minister Barzani's loyal Christian". But Aghajan insists that the Nineveh plains would "get a fairer share" from the Kurdistan administration than from the central government. He praised Barzani's leadership. But he also knows that many Christians are already voting with their feet for the relative safety of Kurdistan.

Then he decribed how his people had been betrayed. "It was easy for the Americans and the British to have supported us when the churches were bombed - it was a historic opportunity - but they did nothing. If they had supported us financially, for example, we could have protected all the Christian families in Mosul."

Asked if he thought the Americans might be afraid to be seen to support the Christians, because that might be perceived as partisan or anti-Muslim, he waved his arm impatiently. "They didn't have to do it publicly - they could have done it through the Kurdistan Regional Government or through individuals. Now the Christians in Mosul are being made to change their religion. They are forced to pay money for jihad. If you hear the stories of those people, you will understand the tragedy. I am not talking about one of two families, or even a thousand, but about a nation.

"If our friends don't help us now, their friendship will be worth nothing in future. If it continues as it has, Baghdad and Mosul will be emptied of Christians."

As he spoke, I recalled Bush's words, over three years ago, from the decks of the USS Abraham Lincoln, announcing "the end of major combat operations" in Iraq. The president is fond of using biblical quotations in his speeches and he ended this one with a stirring message from the prophet Isaiah: "To the captives, 'Come out!' and to those in darkness, 'Be free!'"

In May, Iraq's first full-term government since the fall of Saddam Hussein was approved in Baghdad. Wijdan Mikha'il, a town planner and member of the secular Iraqi National List, was appointed as the new minister of human rights - a hard job, she remarked to me ruefully, in a country where "the people hardly have any rights". Mikha'il is also a Christian, the only one in the government. When she got the job, she moved her family, including her three young boys, from their spacious Baghdad house to live in a hotel behind the concrete blast walls of the Green Zone. Over supper there one evening she talked to me about the sectarianism that has poisoned Iraqi society.

"I have always seen myself as an Iraqi first, and then a Christian. Before, we all lived together, we never thought that someone was a Sunni and the other was a Shia, or a Christian, but now it is different." She has held discussions with the Iraqi Council of Minorities, a new umbrella group that is pushing for amendments to the constitution to improve human rights protection. When I asked Mikha'il about how many Christians were leaving, she said: "The process started before the war but it has accelerated. In the schools the children now say that a Christian is a kaffir, that he is different from the Muslims. And that means he can be treated differently. In 20 years there will be no more Christians in Iraq."

As she talked, two men and two women, dressed mainly in black, walked into the hotel restaurant and sat down in a corner. The minister lowered her voice: "They are Saddam's witnesses." The trial of Saddam Hussein was in session that week, stumbling from one adjournment to the next, and Mikha'il listed some of the atrocities for which the former dictator should still be tried, including the genocidal Anfal campaign against the Kurds, in which many Christians were also killed.

So was it worse before, or now, from the point of view of the Christian community? She replied immediately: "It's worse now. Not just for my community - for all Iraqis. Of course, what is happening now, Saddam partly created. We have gone in one year to a situation we would have reached after 15 years if Saddam was still in power: the lack of security, the breakdown of society . . ." Suddenly she laughed, for the first time that evening. "So maybe it is better to get there in one year, so we can start the process of improvement."

Would she herself still be here in 20 years' time? This time she hesitated. "I don't think so. I love Iraq. I had so many opportunities to leave, but I always stayed. But I don't want my children to live here"