Security forces watched quietly, with shields and batons at their sides.
A group of demonstrators with fuel canisters set a small fire at a compound of a volunteer militia linked to Iran's powerful Revolutionary Guard as the crowd dispersed from the square. As some tried to storm the building, people on the roof could be seen firing directly at the demonstrators at the northern edge of the square, away from the heart of the rally.
An Associated Press photographer saw one person fatally shot and at least two others who appeared to be seriously wounded.
The United States was "deeply troubled" by reports of violence and arrests in Iran, State Department spokesman Ian Kelly said, but he added that the U.S. knows too little about the conduct of the election to say for sure whether there was fraud.
The chanting demonstrators had defied an Interior Ministry ban and streamed into central Tehran - an outpouring for Mousavi that swelled as more poured from buildings and side streets.
The crowd - many wearing the trademark green color of Mousavi's campaign - was more than five miles (nine kilometers) long, and based on previous demonstrations in the square and surrounding streets, its size was estimated to be in the hundreds of thousands.
Mousavi, in a gray striped shirt and talking through a portable loudspeaker, had paused on the edge of the square - where Ahmadinejad made his first postelection speech - to address the throng. They roared back: "Long live Mousavi."
"This is not election. This is selection," read one English-language placard at the demonstration. Other marchers held signs proclaiming "We want our vote!" and raised their fingers in a V-for-victory salute.
"We want our president, not the one who was forced on us," said 28-year-old Sara, who gave only her first name because she feared reprisal from authorities.
Hours earlier, Supreme Leader Ayatollah Ali Khamenei directed one of Iran's most influential bodies, the Guardian Council, to examine the claims. But the move by Khamenei - who had earlier welcomed the election results - had no guarantee it would satisfy those challenging Ahmadinejad's re-election or quell days of rioting after Friday's election that left parts of Tehran scarred by flames and shattered store fronts.
The 12-member Guardian Council, made up of clerics and experts in Islamic law and closely allied to Khamenei, must certify election results and has the apparent authority to nullify an election. But it would be an unprecedented step. Claims of voting irregularities went before the council after Ahmadinejad's upset victory in 2005, but there was no official word on the outcome of the investigation and the vote stood.
More likely, the dramatic intervention by Khamenei could be an attempt to buy time in hopes of reducing the anti-Ahmadinejad anger. The prospect of spiraling protests and clashes is the ultimate nightmare for the Islamic establishment, which could be forced into back-and-forth confrontations and risks having the dissidents move past the elected officials and directly target the ruling theocracy.
The massive display of opposition unity Monday suggested a possible shift in tactics by authorities after cracking down hard during days of rioting.
Although any rallies were outlawed earlier, security forces were not ordered to move against the sea of protesters - allowing them to vent their frustration and wave the green banners and ribbons of the symbolic color of Mousavi's movement.
State TV quoted Khamenei as ordering the Guardian Council to "carefully probe" the allegations of fraud, which were contained in a letter Mousavi submitted Sunday.
On Saturday, however, Khamenei urged the nation to unite behind Ahmadinejad and called the result a "divine assessment."
The results touched off three days of clashes - the worst unrest in Tehran in a decade. Protesters set fires and battled riot police, including a clash overnight at Tehran University after about 3,000 students gathered to oppose the election results.
Security forces have struck back with targeted arrests of pro-reform activists and blocks on text messaging and pro-Mousavi Web sites used to rally his supporters.
One of Mousavi's Web sites said a student protester was killed early Monday in clashes with plainclothes hard-liners in Shiraz, southern Iran. But there was no independent confirmation of the report. There also have been unconfirmed reports of unrest in other cities.
Most media are not allowed to travel beyond Tehran and thus can not independently confirm protests in other cities.
The unrest also risked bringing splits among Iran's clerical elite, including some influential Shiite scholars raising concern about possible election irregularities and at least one member of the ruling theocracy, former President Hashemi Rafsanjani, openly critical of Ahmadinejad in the campaign.
According to a pro-Mousavi Web site, he sent a letter to senior clerics in Qom, Iran's main center of Islamic learning, to spell out his claims.
The accusations also have brought growing international concern. On Sunday, Vice President Joe Biden raised questions about whether the vote reflected the wishes of the Iranian people.
Britain and Germany joined the calls of alarm over the rising confrontations in Iran. In Paris, the Foreign Ministry summoned the Iranian ambassador to discuss the allegations of vote tampering and the violence.
Overnight, police and hard-line militia stormed the campus at the city's biggest university, ransacking dormitories and arresting dozens of students angry over what they say was mass election fraud.
The overnight gathering at Tehran University started with students chanting "Death to the dictator." But it quickly erupted into clashes as students threw rocks and Molotov cocktails at police, who fought back with tear gas and plastic bullets, a 25-year-old student who witnessed the fighting told the AP. He would only give one name, Akbar, out of fears for his safety.
The students set vehicles on fire and hurled stones and bricks at the police, he said. Hard-line militia volunteers loyal to the Revolutionary Guard stormed the dormitories, ransacking student rooms and smashing computers and furniture with axes and wooden sticks, Akbar said.
Before leaving around 4 a.m., the police took away memory cards and computer software material, Akbar said, adding that dozens of students were arrested.
He said many students suffered bruises, cuts and broken bones in the scuffling and that there was still smoldering garbage on the campus by midmorning but that the situation had calmed down.
"Many students are now leaving to go home to their families, they are scared," he said. "But others are staying. The police and militia say they will be back and arrest any students they see."
"I want to stay because they beat us and we won't retreat," he added.
The university was the site of serious clashes against student-led protests in 1999 and is one of the nerve centers of the pro-reform movement.
After dark Sunday, Ahmadinejad opponents shouted "Death to the dictator!" and "Allahu akbar!" - "God is great!" - from Tehran's rooftops. The protest bore deep historic resonance - it was how the leader of the Islamic Revolution Ayatollah Ruhollah Khomeini asked Iran to unite against the Western-backed shah 30 years earlier.
In Moscow, the Iranian Embassy said Ahmadinejad has put off a visit to Russia, and it is unclear whether he will come at all. Ahmadinejad had been expected to travel to the Russian city of Yekaterinburg and meet on Monday with President Dmitry Medvedev on the sidelines of a regional summit.
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