The death toll, which stood at 525, according to the latest Health Ministry figures, makes Wednesday by far the deadliest day since the 2011 popular uprising that toppled longtime ruler and autocrat Hosni Mubarak — a grim milestone that does not bode well for the future of a nation roiled in turmoil and divisions for the past 2 ½ years.
Health Ministry spokesman Khaled el-Khateeb put the number of the injured on Wednesday at 3,717.
Near the site of one of the smashed encampments of ousted President Mohammed Morsi's supporters in the eastern Nasr City suburb, an Associated Press reporter on Thursday saw dozens of blood soaked bodies stored inside a mosque. The bodies were wrapped in sheets and still unclaimed by families.
Relatives at the scene were uncovering the faces in an attempt to identify their loved ones. Many complained that authorities were preventing them from obtaining permits to bury them.
El-Khateeb said 202 of the 525 were killed in the Nasr City protest camp, but it was not immediately clear whether the bodies at the mosque were included in that figure.
Wednesday's violence started with riot police raiding and clearing out the two camps, sparking clashes there and elsewhere in the Egyptian capital and other cities.
Cairo, a city of some 18 million people, was uncharacteristically quiet Thursday, with only a fraction of its usually hectic traffic and many stores and government offices shuttered. Many people hunkered down at home for fear of more violence. Banks and the stock market were closed.
The latest events in Egypt drew widespread condemnation from the Muslim world and the West, including the United States, Egypt's main foreign backer for over 30 years.
Nobel Peace Prize winner Mohamed ElBaradei resigned later Wednesday as Egypt's interim vice president in protest — a blow to the new leadership's credibility with the pro-reform movement.
Interim Prime Minister Hazem el-Beblawi said in a televised address to the nation that it was a "difficult day" and that he regretted the bloodshed but offered no apologies for moving against Morsi's supporters, saying they were given ample warnings to leave and he had tried foreign mediation efforts.
The leaders of Morsi's Muslim Brotherhood called it a "massacre." Several prominent Brotherhood figures were detained as police swept through the two sit-in sites, scores of other Islamists were taken into custody, and the future of the once-banned movement was uncertain.
Backed by helicopters, police fired tear gas and used armored bulldozers to plow into the barricades at the two protest camps on opposite ends of Cairo. Morsi's supporters had been camped out since before he was ousted by a July 3 coup that followed days of mass protests by millions of Egyptians demanding that he step down.
The smaller camp — near Cairo University in Giza — was cleared of protesters relatively quickly, but it took about 12 hours for police to take control of the main sit-in site near the Rabaah al-Adawiya Mosque in Nasr City that has served as the epicenter of the pro-Morsi campaign and had drawn chanting throngs of men, women and children only days earlier.
After the police moved on the camps, street battles broke out in Cairo and other cities across Egypt. Government buildings and police stations were attacked, roads were blocked, and Christian churches were torched, Interior Minister Mohammed Ibrahim said.
At one point, protesters trapped a police Humvee on an overpass near the Nasr City camp and pushed it off, according to images posted on social networking sites that showed an injured policeman on the ground below, near a pool of blood and the overturned vehicle.
Three journalists were among the dead: Mick Deane, 61, a cameraman for British broadcaster Sky News; Habiba Ahmed Abd Elaziz, 26, a reporter for the Gulf News, a state-backed newspaper in the United Arab Emirates; and Ahmed Abdel Gawad, who wrote for Egypt's state-run newspaper Al Akhbar. Deane and Elaziz were shot to death, their employers said, while the Egyptian Press Syndicate, a journalists' union, said it had no information on how Gawad was killed.
The turmoil was the latest chapter in a bitter standoff between Morsi's supporters and the interim leadership that took over the Arab world's most populous country. The military ousted Morsi after millions of Egyptians massed in the streets at the end of June to call for him to step down, accusing him of giving the Brotherhood undue influence and failing to implement vital reforms or bolster the ailing economy.
Morsi has been held at an undisclosed location since July 3. Other Brotherhood leaders have been charged with inciting violence or conspiring in the killing of protesters.
A security official said 200 protesters were arrested at both camps. Several men could be seen walking with their hands up as they were led away by black-clad police.
The Brotherhood has spent most of the 85 years since its creation as an outlawed group or enduring crackdowns by successive governments. The latest developments could provide authorities with the grounds to once again declare it an illegal group and consign it to the political wilderness.
In his televised address, el-Beblawi said the government could not indefinitely tolerate a challenge to authority that the 6-week-old protests represented.
"We want to see a civilian state in Egypt, not a military state and not a religious state," he said.
But the resignation of ElBaradei, the former head of the U.N. nuclear agency and a figure widely respected by Western governments, was the first crack to emerge in the government as a result of the violence.
ElBaradei had made it clear in recent weeks that he was against the use of force to end the protests. At least 250 people have died in previous clashes since the coup that ousted Morsi, Egypt's first freely elected president.
On Wednesday, his letter of resignation to interim President Adly Mansour carried an ominous message to a nation already torn by more than two years of turmoil.
"It has become difficult for me to continue to take responsibility for decisions I disapprove of, and I fear their consequences," he said in the letter that was emailed to The Associated Press. "I cannot take responsibility before God, my conscience and country for a single drop of blood, especially because I know it was possible to spare it.
The National Salvation front, the main opposition grouping that he headed during Morsi's year in office, said it regretted his departure and complained that it was not consulted beforehand. Tamarod, the youth group behind the mass anti-Morsi protests that preceded the coup, said ElBaradei was dodging his responsibility at a time when his services were needed.
Sheik Ahmed el-Tayeb, the powerful head of Al-Azhar mosque, Sunni Islam's main seat of learning, also sought to distance himself from the violence. He said in a statement he had no prior knowledge of the action.