Automatic gunfire echoed across Cairo and black smoke billowed from the capital's huge Ramses Square, yesterday, a military helicopter hovering low overhead looking down on the chaos.
The bodies of 27 people hit by gunfire lay wrapped in white sheets in a mosque. Security forces opened fire from numerous directions when a police station was attacked.
At least 20 people died in clashes elsewhere in Egypt.
The violence followed Wednesday's assault by security forces on two Brotherhood sit-ins in Cairo that left hundreds dead, as the military-backed government tried to end weeks of turbulence that has pushed the Arab world's most populous state to the brink of disaster.
Western governments urged restraint and Germany cautioned the new government that it was reviewing its ties. By contrast, Saudi Arabia's King Abdullah said his country stood with Egypt in its battle against "terrorism".
The army deployed armoured vehicles on major roads around the capital and the Interior Ministry said police would use live ammunition against anyone threatening public buildings.
"Sooner or later I will die. Better to die for my rights than in my bed. Guns don't scare us any more," said Sara Ahmed, 28, a business manager who joined the demonstrators in Cairo. "It's not about the Brotherhood, it's about human rights," she said, one of the few women in the crowd not wearing a headscarf, a sign of piety for Muslim women.
Anger on the streets was directed at army commander General Abdel Fattah al Sisi, who moved against Mr Mursi last month after massive street rallies against an administration accused of incompetence and partisanship.
"The people want the butcher executed," said Mustafa Ibrahim, 37, of Gen Sisi as a crowd of several thousand marched on central Cairo.
Emergency services said eight protesters were killed in clashes in the Mediterranean town of Damietta, five in Fayoum south of Cairo, four in the Suez Canal city of Ismailia and four in the Nile delta town of Tanta. One was killed in Alexandria, Egypt's second city.
A police conscript was killed in a drive-by shooting in the north of the capital. Nile TV showed footage of a gunman among Islamist protesters firing from a central Cairo bridge.
Signalling his displeasure at the worst bloodshed in Egypt for generations, US President Barack Obama said normal co-operation with Cairo could not continue and cancelled military exercises with Egypt next month.
"We deplore violence against civilians. We support universal rights essential to human dignity, including the right to peaceful protest," he said, but stopped short of cutting off the $1.5 billion (£960bn) a year of mostly military US aid to Egypt.
The Brotherhood accuses the military of staging a coup when it ousted Mr Mursi in July. Liberal and youth activists who backed the military saw the move as a positive response to public demands.
However, some fear Egypt is turning back into the kind of police state that kept former president Hosni Mubarak in power for 30 years before his removal in 2011, as security institutions recover their confidence and reassert control.
In calling for a "Day of Rage," the Brotherhood used the same name as that given to the most violent day of the uprising against Mr Mubarak.
Ironically, the centre of the anti-Mubarak protests, Tahrir Square, was deserted yesterday, sealed off by the army.