The conflict now besetting the middle east is, like all major international conflicts, multidimensional. It involves not just one major axis of violence (Israel/Arabs, United States/terrorism, west/Iran) but several overlapping conflicts that draw states and armed movements into their arena. The major concern of strategists and analysts remains the polarisation between the US and its foes in Iraq and, increasingly, in Iran. But there is another important, ominous, conflict accompanying these that has little to do with the machinations of Washington or Israel, and is less likely to be contained by political compromise: the spread, in a way radically new for the middle east, of direct conflict between Sunni and Shi'a Muslims.

Many generalisations and simplifications accompany the whole issue of Sunni and Shi'a Islam. In the aftermath of the Iranian revolution, when Ayatollah Khomeini produced a radical, populist, third-world rhetoric that denounced the west and the "golden idols" or taghut who served imperialist interests in the region (among them the Shah of Iran, Anwar Sadat, Saddam Hussein, and the Gulf rulers), it was claimed by many that Shi'ism, the belief of around 10% of all Muslims, was inherently militant.

Unlike the Sunni, who had historically accepted the legitimacy of Islamic rulers, the caliphs, and who paid their clergy from state funds, thereby controlling them, the Shi'a refused to accept the Muslim credentials of their rulers and produced a clergy, paid for by the subscriptions of the faithful, that were closer to the people and so more radical.

I recall a conversation with Ibrahim Yazdi, the first foreign minister of the Islamic Republic of Iran (who after Ayatollah Khomeini's death spent years under virtual house arrest in Tehran). As he sat under the enormous chandeliers of what had been the Shah's foreign ministry, he exclaimed with pride: "We are the Trotskyists of Islam!"

The logic of Yazdi's characterisation - with its echoes of the Russian revolutionary leader's theory of "permanent revolution" - was to spread Iran's radical anti-imperialism across the region: a force far superior, in his view, to the then vacillating as well as pro-Soviet ideology of the secular left.

Much of this was simplistic and one-sided: like all bodies of religious text and tradition, Shi'a and Sunni beliefs are liable to many interpretations. Iran has chosen, however, to put a militant stamp on its beliefs and, in a revolution that has far from run its course, to promote these values across the Muslim world. Today, this international radicalism of the Iranian revolution has come to be an explosive force in the middle east: directed on one side against the United States, but in a dangerous inflaming of communal relations, against Sunni Muslims as well.

Fred Halliday is professor of international relations at the LSE, and visiting professor at the Barcelona Institute of International Studies (IBEI). His books include Islam and the Myth of Confrontation (IB Tauris, 2003) and 100 Myths About the Middle East (Saqi, 2005)

Fred Halliday's "global politics" column on openDemocracy surveys the national histories, geopolitical currents, and dominant ideas across the world. The articles include:

"America and Arabia after Saddam"
(May 2004)

"Iran's revolutionary spasm" (July 2005)

"Political killing in the cold war" (August 2005)

"Maxime Rodinson: in praise of a 'marginal man'"
(September 2005)

"A transnational umma: myth or reality? " (October 2005)

"The 'Barcelona process': ten years on" (November 2005)

"Iran vs the United States – again" (February 2006)

"A Lebanese fragment: two days with Hizbollah" (July 2006)

"Fidel Castro's legacy: Cuban conversations" (August 2006)

"España: memory for the future"
(20 October 2006)

"The end of the Vatican" (5 December 2006)

"Expecting rain: a letter from Jerusalem"
(15 December 2006)

"A 2007 warning: the twelve worst ideas in the world"
(8 January 2007)

"Auschwitz's 21st-century legacy" (26 January 2007)

The paths of conflict

This communal conflict is evident most of all in Iraq. What began in 2003 as a largely Sunni and former Ba'athist rising against the American forces and their Iraqi allies had by mid-2006 developed into a multi-sided conflict in which Sunni and Shi'a forces were in conflict with the Americans but also increasingly with each other. By early 2007 it is estimated that up to 2 million people have been displaced by the war, equally divided between those fleeing to other parts of Iraq and those forced into exile.

This Iraqi sectarian war has echoes - if the consequences are as yet far less bloody - elsewhere in the region:

• in the Gulf states, notably Kuwait and Bahrain, where relations between the Shi'a and Sunni populations of these states (respectively a quarter and a half of the total population) have worsened

• in Lebanon, where the forward advance of Hizbollah during and after the summer 2006 war led to worsened relations with the Sunni population, although not - even amid political tumult - to direct conflict

• in Palestine, where there are no Shi'a, supporters of Fatah nonetheless took to denouncing the supporters of Hamas as "Shi'a" on account of the movement's links to Iran.

In Syria matters are less overt, but it is no secret that for decades the Sunni majority of the population had resented rule by an Alawi elite of Shi'a origin, represented in the Ba'ath party, who had controlled the country since 1963. The one direct challenge to the Ba'athists by the Sunni, in the form of a Muslim Brotherhood insurrection centred on the city of Hama, was crushed with great brutality by Hafez al-Assad's forces in 1982; but two decades later, the Muslim Brotherhood have regained considerable influence in the country, especially amongst the Sunni middle classes. The movement would be the main beneficiary of any fatal crisis of the Bashar al-Assad regime.

Against this background it was not surprising that some Arab leaders - notably those of Egypt, Jordan and Saudi Arabia - began to warn of the dangers of the advance of Iranian and Shi'a power and to present themselves as a "moderate" Muslim bulwark against the advance of the revolutionary Shi'a alliance.

At the level at which it has been developing in 2006 and early 2007, it is possible to envisage this conflict between Sunni and Shi'a as becoming the dominant regional fracture in the ensuing period - especially amidst a withdrawal, at whatever pace, of American forces from Iraq.

In such conditions, there are many analysts or propagandists who resort to the notion that this sectarianism is a "deep structure", reflecting a latent atavism that has long underlain the politics of the region. The implication is that the overt violence of 2006-07 involves the emergence to the surface of deep and ever-present, hatreds. (Similar arguments about "ancient ethnic hatreds" were heard repeatedly in the context of the wars in Yugoslavia, Sri Lanka, and Northern Ireland).

However, another analysis is more persuasive. This sees the Sunni-Shi'a conflict as essentially a recent development, a product of the middle-east political crisis in recent decades and, in the case of Iraq, of the spiral of violence released by the United States invasion of 2003. In this perspective, the origins of the conflict - and more generally of the Arab-Persian conflict - lie not in ancient hostility and grievance, but in the modern history of the region; in particular, the ways in which the twin revolutions of Iraq (1958) and Iran (1979) set in motion rivalry and insecurity between states and peoples that exploded first in the Iran-Iraq war of 1980-88, and again, inside Iraq, from 2003.

The twist of modernity

At the same time, two cautionary observations are in order. First, in terms of religious belief there is no deep divide, because there is little to be divided about. The actual religious, theological, distinctions between Sunni and Shi'a are small, far less than those between Catholics and Protestants within Christianity.

They revolve not so much around questions of belief or even interpretation of holy texts, but around rival claims to legitimacy and succession in the aftermath of the Prophet Mohammed's death in 632 CE, with Sunni favouring the "successors" or "caliphs" and Shi'a seeing succession in the prophet's son-in-law Ali, the latter's son Hussein, and those who come after them.

The death of Hussein at the battle of Karbala (661) at the hands of the Umayyad caliph Yezid is taken as the founding moment of Shi'ism, to which all later historical legitimation, and annual mourning ceremonies, refer. One of the major complaints of Sunni against Shi'a is that preachers in the latter's mosques curse the early successors of the prophet, the caliphs revered by Sunni. But this 7th-century division does not account for the major conflicts of the Islamic world then or later, in a way that wars between Catholic and Protestant were to do in early-modern Europe.

There were, moreover, forms of coexistence and interaction between the two which find little parallel in Europe. These include widespread intermarriage (in Iraq as elsewhere), and the use even of places of worship associated with one confession by followers of the other group. The Sayyidna al-Hussein mosque in Cairo, built by the Fatimid medieval Shi'a dynasty that ruled Egypt at the time is also revered by Sunni; the Umayyad mosque in Damascus, the most historically important in the Sunni world, has a section devoted to the commemoration of Hussein, to which Shi'a visitors from Iran regularly make pilgrimage.

Second, actual and direct conflict between Sunni and Shi'a (as distinct from suspicion and communal difference) has until recently been remarkable by its absence. What is more evident is differential political loyalty between the communities, in relation to (for example) Arab nationalism, secularism, or the Iranian revolution. It has moreover, been possible to identify particular Muslim ruling elites as either Sunni or Shi'a: Sunni in most cases, but Shi'a in Iran, Yemen, and Syria.

Yet even here, where a sectarian element clearly entered into the distribution of power, it did not spark a revolt based on sectarianism itself. Thus the Kurds in Iran are mainly Sunni, a fact that no doubt contributed to their resistance to the Shi'a state created by Khomeini after 1979. In Iraq, the Shi'a rose up in 1991 against Saddam, but this was in conjunction with the Kurds, on a mainly national political basis - and even as Saddam replied by crushing the uprising under the slogan La Shi'a Ba'ad al Yaum (No Shi'a From Today). In the case of Iraq, the Sunni monopoly was partly broken once before 2003, in the person of the first president after the revolution of 1958, Abd al-Karim Qasim, who was half Sunni, half Shi'a, but seen as favouring the latter.

Where it has occurred in recent decades, overt conflict and sectarian violence between Sunni and Shi'a originated first not in the Arab world or Iran, but further east, in Pakistan and Afghanistan. In the former, its encouragement became in the 1970s part of the ideology of militant Sunni groups associated with guerrilla action in Kashmir, and later in Afghanistan, to promote hostility to Shi'a; from the 1980s onwards there were regular attacks on Shi'a mosques in different parts of Pakistan. In the Afghan wars of the 1980s and 1990s, the militant Sunni groups who dominated the mujahideen came to attack the Shi'a community of Afghanistan as enemies of their cause (see "America and Arabia after Saddam", 13 May 2004).

This radical Sunni rhetoric charged that, because they worshipped the shrines of imams and other holy men, the Shi'a were defectors from the monotheism of Islam and, in effect, "polytheist". Indeed in some bizarre versions, the term for polytheist, moshrik ("one who shares") came to be used as a synonym for "communist", in the sense of someone who shared property in common.

The final twist in this saga involved the creation of a cult, by the Taliban in Afghanistan, of the 10th-11th-century leader Sultan Mahmud, a man whose main claim to fame was that he had invaded India "a hundred times": his grave in Ghazni was used as a shrine for young Taliban soldiers being sent to fight Shi'a, where, they were told, Sultan Mahmud "was killing communists, even in the time of the prophet". Such ideological invention and redefinition is central to the contemporary conflict of Sunni and Shi'a. It involves the use on both sides of terms of abuse and historical delegitimation that, while they have historical precedent, have needed to be recreated as bearers of modern identity and confrontation.

The worst of all

Modernity, and the use of communal or religious differences for contemporary political ends, are however no barrier to the spread of hatred and violence. These fires, once lit, can destroy forms of coexistence that have existed for centuries. This is clearly the case in the "war of elimination" in Baghdad today (a city from which, it may be recalled, the Jewish community who had lived there for over two millennia experienced a mass exodus in the early 1950s).

Moreover, while at the beginning states may seek to control such sectarian loyalties, as both Iran and Saudi Arabia have done, such control may not last: today Iran has much less influence over the Shi'a of Iraq than it had three or ten years ago. How far these flames will spread is anyone's guess, but it would seem that the invasion of Iraq has set off a dangerous dynamic that could affect much of the region. The US and its allies are certainly wondering which way the Arab and Sunni world will jump in the event of an attack on Iran.

Some may take comfort from the dire warning that issued from a conference of Sunni and Shi'a clergy recently held in Qatar. As representatives of each side promised to stop preaching suspicion of the other, and Shi'a committed themselves to stop cursing the caliphs, a prominent Iraqi cleric warned that if this conflict were to continue, the direst of all consequences would follow: namely that young people in the Muslim world would be tempted ... to turn to secularism.