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The Convent of Our Lady of Seidnaya is a Greek Orthodox convent in Seidnaya, Syria, three hours’ walk from Damascus. The monastery sits on a great crag of rock overlooking the orchards and olive groves of the Damascene plain, and at first sight, with its narrow windows and great rugged curtain walls, looks more like a Crusader castle than a convent.

According to legend, the monastery was founded in the early sixth century after the Byzantine Emperor Justinian chased a stag onto the top of the hill during a hunting expedition. Just as Justinian was about to draw his bow, the stag changed into the Virgin Mary, who commanded him to build a convent on the top of the rock. The site, she said, had previously been hallowed by Noah, who had planted a vine there after the flood.

Partly because of this vision, and partly because of the miracle-working powers of one of the convent's icons, said to have been painted by St. Luke himself, the abbey quickly become a place of pilgrimage and to this day streams of Christian, Muslim and Druze pilgrims trudge their way to Seidnaya from the mountains of Lebanon and the valleys of the Syrian jebel. In 1994, while on a six-month tramp around the Middle East, I went to spend a night within its walls.

By the time I arrived at the monastery gate, it was after eight o'clock on a dark and cold winter's night. Walking into an empty courtyard, my feet echoing on the flagstones, I wondered for a second where everyone had gone. Then I heard the distant sound of Orthodox chant drifting from the church and headed towards it.

Two nuns in black veils were chanting from a lectern, while a priest, hidden behind the iconostasis, echoed their chants in a deep reverberating bass. The only light came from a few flickering lamps suspended from the ceiling on gold chains. As the candlelight waxed and waned in the breeze, the highlights of the frescoes in the domes and semi-domes flashed momentarily into view then disappeared again into the shadows.

When a friend of mine visited the convent thirty years ago, he said he witnessed a miracle: that he saw the face of the icon of Notre Dame de Seidnaya stream with tears. In the same church I too witnessed a miracle, or something that today would certainly be regarded as a miracle in almost any other country in the Middle East. For the congregation in the church consisted not principally of Christians but almost entirely of heavily bearded Muslim men and their shrouded wives. As the priest circled the altar with his thurible, filling the sanctuary with great clouds of incense, the men bobbed up and down on their prayer mats as if in the middle of Friday prayers in a great mosque. Their women, some dressed in full black chador, mouthed prayers from the shadows of the exo-narthex. A few, closely watching the Christian women, went up to the icons hanging from the pillars; they kissed them, then lit a candle and placed it in the candelabra in front of the image. As I watched from the rear of the church I could see the faces of the women reflected in the illuminated gilt of the icons.

Towards the end of the service, the priest circled the length of the church with his thurible, gently and almost apologetically stepping over the prostrate Muslims blocking his way. It was a truly extraordinary sight, Christians and Muslims praying together in a fashion unimaginable today almost anywhere else in the Near East. Yet it was, of course, the old way: the Eastern Christians and the Muslims have lived side by side for nearly one and a half millennia and have only been able to do so due to a degree of mutual tolerance and shared customs unimaginable in the solidly Christian West.

How easy it is today to think of the West as the home of freedom of thought and liberty of worship, and to forget how, as recently as the seventeenth century, Huguenot exiles escaping religious persecution in Europe would write admiringly of the policy of religious tolerance practised across the Islamic world: as M de la Motraye put it, 'there is no country on earth where the exercise of all Religions is more free and less subject to being troubled, than in Turkey'. The same broad tolerance that had given homes to the hundreds of thousands of penniless Jews expelled by the bigoted Catholic kings from Spain and Portugal, protected the Eastern Christians in their ancient homelands - despite the Crusades and the almost continual hostility of the Christian West. Only in the twentieth century has that tolerance been replaced by a new hardening in Islamic attitudes; and only recently has the syncretism and pluralism of Seidnaya become a precious rarity.

As vespers drew to a close the pilgrims began to file quietly out and I was left alone at the back of the church with my rucksack. As I was standing there I was approached by a young nun. Sister Tecla had intelligent black eyes and a bold, confident gaze; she spoke fluent French with a slight Arabic accent. I remarked on the number of Muslims in the congregation and asked: was it at all unusual?

"The Muslims come here because they want babies," said the nun simply. "Our Lady has shown her power and blessed many of the Muslims. The people started to talk about her and now more Muslims come here than Christians. If they ask for her she will be there."

As we were speaking, we were approached by a Muslim couple. The woman was veiled - only her nose and mouth were visible through the black wraps; her husband, a burly man who wore his beard without a moustache, looked remarkably like the wilder sort of Hezbollah commander featured in news bulletins from Southern Lebanon. But whatever his politics, he carried in one hand a heavy tin of olive oil and in the other a large plastic basin full of fresh bread loaves, and he gave both to the nun, bowing his head as shyly as a schoolboy and retreating backwards in blushing embarrassment.

"They come in the evening, " continued the nun. "They make vows and then the women spend the night. They sleep on a blanket in front of the holy icon of Our Lady. Sometimes the women eat the wick of a lamp that has burned in front of the image, or maybe drink the holy oil. Then in the morning they drink from the spring in the courtyard. Nine months later they have babies."

"And it works?"

"I have seen it with my own eyes," said Sister Tecla. "One Muslim woman had been waiting for a baby for twenty years. She was beyond the normal age of childbearing but someone told her about the Virgin of Seidnaya. She came here and spent two nights in front of the icon. She was so desperate she ate the wicks of nearly twenty lamps."

"What happened?"

"She came back the following year," said Sister Tecla, "with triplets."

The nun led me up the south aisle of the church, and down a corridor into the chapel which sheltered the icons. It was darker than the church, with no windows to admit even the faint light of the moon, which had cast a silvery light over the altar during vespers. Here only the twinkling of a hundred lamps lit the interior, allowing us to avoid tripping over a pair of Muslims prostrated on their prayer carpets near the entrance. Sister Tecla kissed an icon of the warrior saints Sergius and Bacchus, then turned back to face me: "Sometimes the Muslims promise to christen a child born through the Mother of God's intervention. This happens less frequently than it used to, but of course we like it when it does. Others make their children Muslims, but when they are old enough they bring them here to help us in some way, cleaning the church or working in the kitchens."

I was in the Middle East researching From the Holy Mountain, a book on what I believe is one of the great unrecorded tragedies of the late twentieth century: the slow death of the ancient Christian communities of the Holy Land. These Eastern Christian churches are the descendants of the apostles and very first Christians, and for two thousands years they have managed to cling on in what has always been one of the most turbulent regions of the earth. But now their struggle for survival seems to be coming to an end.

Right across Middle East things are suddenly becoming difficult for the last Christians. Almost everywhere in the Levant, for a variety of different reasons - partly because of economic pressure, but more often due to discrimination and in some cases outright persecution - the Christians are leaving. Today in the Middle East they are a small minority of 14 million struggling to keep afloat amid 180 million non-Christians, with their numbers shrinking annually through emigration. In the last 20 years at least two million have left to make new lives for themselves in Europe, Australia and America.

In Istanbul the last descendants of the Byzantines are now leaving what was once the capital city of Christendom. In the East of Turkey, the Syrian Orthodox church is virtually extinct; its ancient monasteries are now either empty or in the process of being evacuated. In Lebanon, the Maronites have now effectively lost the long Civil War, and their stranglehold on political power has finally been broken. Most Maronites today live abroad, in exile. The same is true of the Palestinian Christians, a little to the South: nearly half a century after the creation of the State of Israel, fewer Palestinian Christians now remain in Palestine than outside it. Things have got so bad that the remaining Christians in Jerusalem could be flown out in just nine jumbo jets; indeed there are now said to be more Jerusalem-born Christians living in Sydney than in Jerusalem itself. In Egypt, the Copts are also apprehensive: already facing a certain amount of discrimination under the current regime, they are well aware that things are likely to get much worse if President Mubarak falls and the fundamentalists come to power.

As I made my way through the Middle East I found no shortage of examples of discrimination against Christians, but as at Seidnaya I also found myself constantly reminded of what was in many ways a more surprising story altogether: the amazing way in which Christians and Muslims had, until recently, succeeded in living together for so many centuries, in closely knit communities in town after town, village after village across the Middle East. If that coexistence was not always a complete harmony, it was at least, with very few exceptions, a kind of pluralist equilibrium.

Across the length of what was once the former Ottoman Empire the twentieth century has seen, with the rise of education, self-consciousness and modern nationalism, the bloody unravelling of that complex tapestry - most recently and painfully in Bosnia, but before that in Cyprus, Palestine, Greece and Turkey. In each of these places pluralism has been replaced by a savage polarisation. In drips and drabs, and sometimes in great tragic exoduses, religious minorities have fled to places where they can be majorities, and those too few for that have fled the region altogether, seeking out places less heavy in history such as America and Australia. If the twentieth century has seen Europe change to a multicultural society, the same period has seen country after country in the Middle East change in the opposite direction, to a series of monolithic monoethnic blocks.

Only in a few places such as Syria does the old intricate patchwork survive, but in these areas the old ways can be found surviving still. Shortly after seeing Muslims coming en masse to pray in the Christian basilica at Seidnaya, I saw Christians coming to sacrifice a sheep at the shrine of a Muslim saint in the ruins of the old Byzantine city of Cyrrhus, north west of Aleppo. I was told that a Syrian Orthodox girl struck down by some apparently incurable sickness had had a dream telling her to visit the shrine of Nebi Uri at Cyrrhus. She had done so, spent the night in his shrine, and the next day had been healed. The sheep, which was covered with flowers and ribbons like the Old Testament scapegoat, was being slaughtered as an offering.

"We believe that if you are generous and give a good sheep to fulfil your vow," said the Sufi Sheik who presided over the shrine, "then you will ride that sheep at the Day of Judgement. That sheep will carry you into Paradise."

"And the Christians believe this too?" I asked

"There is no difference between ourselves and the Christians on this matter," said the Sheik, "except that sometimes the Christians make the sign of Christ over the forehead of the person want cured."

Again and again in the Middle East I came across this extraordinary Christian-Muslim syncretism, this porousness of faith, where the ideas, practices and superstitions of one religion have trickled imperceptibly into another. But there was something else too. It wasn't just that in many places Christianity and Islam were still managing to coexist: seeing them together, and seeing the way the Eastern Christians practised their faith, brought home quite how closely the two faiths are really linked.

Today the West often views Islam as a civilisation very different from and indeed innately hostile to Christianity. Only when you travel in Christianity's Eastern homelands do you realise how closely the two are really connected, the former growing directly out of the latter and still, to this day, embodying many aspects and practices of the early Christian world now lost in Christianity's modern Western-based incarnation. When the early Byzantines were first confronted by the Prophet's armies, they assumed that Islam was merely an heretical form of Christianity, and in many ways they were not so far wrong: Islam accepts much of the Old and New Testaments and venerates both Jesus and the ancient Jewish prophets.

Significantly, the greatest and most subtle theologian of the early church, St. John Damascene, was convinced that Islam was at root not a separate religion, but instead a form of Christianity. St. John had grown up in the Ummayad Arab court of Damascus, where his father was chancellor, and he was an intimate boyhood friend of the future Caliph al-Yazid; the two boys’ drinking bouts in the streets of Damascus were the subject of much horrified gossip in the streets of the new Islamic capital. Later, in his old age, John took the habit at the desert monastery of Mar Saba where he began work on his great masterpiece, a refutation of heresies entitled the Fount of Knowledge. The book contains an extremely precise and detailed critique of Islam, the first ever written by a Christian, which, intriguingly, John regarded as a form of Christian heresy related to Arianism: after all Arianism, like Islam, denied the divinity of Christ. Although he lived at the very hub of the early Islamic world, it never seems to have occurred to him that Islam might be a separate religion. If a theologian of the stature of John Damascene was able to regard Islam as a new- if heretical- form of Christianity, it helps to explain how Islam was able to convert so much of the Middle Eastern population in so short a time, even though Christianity remained the majority religion until the time of the Crusades.

The longer you spend in the Christian communities of the Middle East, the more you become aware of the extent to which Eastern Christian practice formed the template for what were to become the basic conventions of Islam. The Muslim form of prayer with its bowings and prostrations appears to derive from the older Syrian Orthodox tradition that is still practised in pewless churches across the Levant. The architecture of the earliest minarets, which are square rather than round, unmistakably derive from the church towers of Byzantine Syria. The Sufi Muslim tradition carried on directly from the point that the Christian Desert Fathers left off while Ramadan, at first sight one of the most foreign and alienating of Islamic practices, is in fact nothing more than an Islamicisation of Lent, which in the Eastern Christian churches still involves a gruelling all-day fast.

Certainly if a monk from sixth century Byzantium were to come back today it is probable that he would find much more that was familiar in the practices and beliefs of a modern Muslim Sufi than he would with, say, a contemporary American Evangelical. Yet this simple truth has been lost by our tendency to think of Christianity as a thoroughly Western religion rather than the Oriental faith which by origin it actually is. Moreover the modern demonisation of Islam in the West, particularly since the Second World War and the foundation of the western-backed State of Israel, together with the recent growth of Muslim fundamentalism (itself in many ways a reaction to the West's repeated humiliation of the Muslim world) have led to an atmosphere where few in either camp are aware of, or indeed wish to be aware of, the profound kinship of Christianity and Islam.

It is this as much as anything else that has made the delicate position of the contemporary Eastern Christians increasingly untenable in recent years, as they find themselves awkwardly caught between their co-religionists in the West and their strong cultural links with their Muslims compatriots. Hence the vital importance of the popular syncretism which still exists at shrines like Seidnaya and Cyrrhus, and which was once much more general across the Middle East. The practice emphasises an important truth about the close affinity of the two great religions easily forgotten as the Eastern Christians- the last surviving bridge between Islam and Western Christianity- emigrate in reaction to the increasing hostility of the Islamic establishment.

Yet this kinship between the different religions of the book is something Muslim writers have been aware of for centuries. The thirteenth century Sufi Jalal-ud Din Rumi, perhaps the greatest of all the mystical writers of Islam, lived in a town in Central Anatolia in which the population was almost equally divided between Muslims, Christians and Jews. When he was asked about the relationship between these three apparently incompatible religions, he replied with the following story:

"Once upon a time, in a far distant country somewhere north of Afghanistan, there was a city inhabited entirely by the blind. One day the news came that an elephant was passing outside the walls of the city.

"The Citizens called a meeting and decided to send a delegation of three men outside the gates so that they could report back what an elephant was. In due course the three men left the town and stumbled forwards until they eventually found the elephant. The three reached out, felt the animal with their hands, then they all headed back to town as quickly as they could to report what they had felt.

"The first man said: "An elephant is a marvellous creature! It is like a vast snake, but it can stand vertically upright in the air!" The second man was indignant at hearing this: "What nonsense!" he said. "This man is misleading you. I felt the elephant and what it most resembles is a pillar. It is firm and solid and however hard you push against it you could never knock it over." The third man shook his head and said: "Both these men are liars! I felt the elephant and it resembles a broad fan. It is wide and flat and leathery and when you shake it wobbles around like the sail of a dhow." All three men stuck by their stories and for the rest of their lives refused to speak to each other. Each professed that they and only they knew the whole truth.

"Now of course all three of the blind men had a measure of insight. The first man felt the trunk of the elephant, the second the leg, the third the ear. All had been granted part of the truth, but not one of them had begun to grasp the totality or the greatness of the beast they had encountered. If only they had listened to one another and meditated on the different facets of the elephant, they might have grasped the true nature of the beast. But they were too proud and instead preferred to keep to their own half truths.

"So it is with us. We see Allah one way, the Jews have a slightly different conception, and the Christians have a third. To us, all our different visions are irreconcilable. But what we forget is that before God we are like blind men stumbling around in total darkness..."

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