The bomb attack has enraged the majority Shia population, who regard the shrine in the same way that Roman Catholics view St Peter's in Rome.
In a number of respects civil war in Iraq has already begun. Many of the thousand bodies a month arriving in the morgues in Baghdad are of people killed for sectarian reasons. It is no longer safe for members of the three main communities the Sunni and Shia Arabs and the Kurds to visit each other's parts of the country.
"Iraq is in a Weimar period like Germany in the 1920s which will either end with the country disintegrating or in an authoritarian government taking power," said Ghassan Atiyyah, an Iraqi political commentator.
The Golden Mosque in Samarra, north of Baghdad, was attacked at 6.55am yesterday when men dressed in police uniform tied up the guards and planted explosives. It was the third and most devastating attack on the Shia in Iraq in three days. A car bomb had killed 22 people in a Shia district of Baghdad late the previous night. The day before 12 died when a suicide bomber blew himself up in a bus in the Shia stronghold of Khadamiyah in west Baghdad.
"We should stand hand in hand to prevent the danger of civil war," warned President Jalal Talabani. "We are facing a major conspiracy that is targeting Iraq's unity." He called for the formation of a national unity government that "will bring stability to Iraq".
There was little sign of stability yesterday. Some 50 Sunni mosques were either burnt, blown up or taken over in Baghdad alone. At least three Sunni clerics were among 22 reported deaths nationwide.
Gunmen in police uniforms seized a dozen Sunni men suspected of being insurgents from a prison in the mainly Shia city of Basra yesterday and later killed 11 of them. Among those killed in the apparent reprisal attack for the bombing of the Samarra shrine were two Egyptians.
Armed militiamen of the Mehdi Army supporting the radical nationalist clergyman Muqtada al-Sadr took up positions on the streets of Baghdad and in the Shia cities of the south yesterday. Mr Al-Sadr himself is returning quickly to Iraq after cancelling a meeting with the Lebanese President. One of his aides said: "If the Iraqi government does not do its job to defend the Iraqi people, we are ready to do so." A Sunni politician, Tariq al-Hashimi, urged clerics and politicians to calm the situation " before it spins out of control".
As news spread of sectarian clashes and demonstrations people in Baghdad rushed home before dark and some started to stock up on food. In Najaf, another Shia holy city, protesters chanted: "Rise up Shia! Take revenge! "
The destruction of the Golden Mosque will be an immense psychological blow to Iraqi Shia who have endured so much down the centuries. The shrine contains the tombs of the 10th and 11th imams, Ali al-Hadi who died AD868 and his son Hassan Ali al-Askari who died AD874. His son, the last of the 12 Shia imams, Mohammed al-Mahdi, disappeared and is known as the "hidden imam". Shias believe he is still alive and will bring justice to humanity.
The shrine is very difficult to defend. The majority of people in Samarra are Sunni and in 2004 the city was taken by Islamic extremists before being recaptured by the Americans. Although I was searched the last time I visited the mosque, it has large gateways through the outer wall into an inner courtyard which armed men would find easy to storm. The shrine guards, who might detect a single bomber, were evidently not able to stop a unit of armed and determined men posing as police.
In one of the most serious acts of retaliation Shia protesters set fire yesterday to a famous Sunni shrine on the outskirts of Basra. It contains the tomb of Talha bin-Obeid-Allah, a companion of the Prophet Mohamed. The extent of the damage was not known.
Iraq has always been riven by sectarian divisions. Saddam Hussein's regime was primarily Sunni, though they are only 20 per cent of the population, while the Shia were politically marginalised. Friction between Shia and Sunni has increased since the US invasion as the Sunni resisted the occupation while the Shia demanded elections which they were bound to win because they are a majority of the population. If the Shia do hold power it will be the first time they have had their own state in the Arab world since the 12th century.
The parliamentary election on 15 December confirmed the Shia dominance, with their coalition winning 128 out of 275 seats. The vote was almost entirely along sectarian or ethnic lines.
The Shia clerical leader, Grand Ayatollah Ali al-Sistani, called for a week of mourning, forbade attacks on Sunni mosques and asked people to protest peacefully. He made a rare appearance on television yesterday, being shown meeting in his house in Najaf three other grand ayatollahs to discuss the destruction of the mosque in Samarra. There was no audio but a statement from Ayatollah Sistani's office said: "We call upon believers to express their protest ... through peaceful means. The extent of their sorrow and shock should not drag them into taking actions that serve the enemies who have been working to lead Iraq into sectarian strife."
In the past his appeals for calm have been heeded, despite a long series of atrocities by suicide bombers against the Shia beginning in August 2003 which has left several thousand dead.
There are signs that the Shias' patience is now growing thin. Death squads targeting Sunni operate in Baghdad.
The prolonged negotiations to form a new government underlines the difficulty the Shia, Kurds and Sunni are having in reaching an accommodation which will hold Iraq together. The Kurds have always demanded a degree of autonomy under a federal system which would give them quasi-independence. Under the constitution supported in a referendum by Kurds and Shia last October, the nine Shia provinces of the south would also become a canton largely independent of Baghdad. One Iraqi minister laments that "the Iraqi government may end up as a collection of buildings in the Green Zone".
Although the US and the Kurds are demanding a national unity government, Shia leaders suspect that this is a manoeuvre by the US to keep them out of power. Washington has long been worried that the outcome of its invasion and overthrow of Saddam would be a Shia-dominated Islamic republic closely linked to Iran. It is also concerned with the rise of Mr al-Sadr, always against the occupation, to the position of power broker in the Shia coalition.
There are signs of increasing anti-American feeling among the Shia as they see the Americans allying themselves with the Sunni. As news spread of the attack on the Golden Mosque yesterday, thousands of young men marched shouting anti-American slogans through Sadr City, the great Shia slum with a population of two million. About 3,000 people marched through the Shia city of Kut shouting slogans against America and Israel and burning US and Israeli flags.
The extent of Shia retaliation may also depend on the Iranian government. The Iranian supreme leader, Ayatollah Ali Khamenei, urged Shia not to seek revenge against Sunni Muslims, saying there were definite plots "to force the Shia to attack the mosques and other properties respected by the Sunni. Any measure to contribute to that direction is helping the enemies of Islam and is forbidden by sharia."
Instead Ayatollah Khamenei blamed the intelligence services of the US and Israel for being behind the bombs in Samarra.
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