Large numbers of armed troops and security forces were said to be on the streets of Damascus to quell protests, with tear gas used as prayers ended.
Rallies were reported in Homs, in the north and in coastal cities.
Activists had called for a "day of rage" and solidarity with victims of a recent crackdown in the city of Deraa.
A resident of Deraa, where protests have been strongest, told the BBC two people had been killed there on Friday, but this could not be independently confirmed.
The city has endured days without power and is reported to be "locked down".
In Deraa, troops were said to have fired in the air and were intimidating residents to stay indoors.
"They will open fire if you leave your house," one resident told Reuters news agency.
Syrian state media said four soldiers had been killed and two others captured in a "terrorist" attack on their post in Deraa on Friday. The report cannot be verified.
Activists and human rights groups say the recent crackdown on anti-government dissent has left some 500 people dead.
There has been growing international criticism of the response to protests against the regime of President Bashar al-Assad.'Chant for freedom'
EU officials are meeting in Brussels on Friday to discuss sanctions against President Bashar al-Assad's regime, while the UN Human Rights Council is holding an emergency meeting in Geneva on Syria.Continue reading the main story Jim Muir BBC News, Beirut
The situation in Deraa is clearly becoming increasingly desperate. Around 120,000 people are trapped there.
Since Monday, they've been isolated by thousands of government troops and dozens of tanks. Water, electricity and phones have been cut off all that time. There are no medicines, and no access to medical facilities.
Demonstrations and shootings are reported from other parts of the country, with some Syrians even fleeing into Lebanon on foot to get away.As has become typical during months of protests in a number of Middle East countries, Friday was billed as a "day of rage" in Syria.
Protests flared in several Damascus suburbs, including Daraya, and tear gas was used as crowds left the Zein al-Bedin mosque in the capital's Median area, according to reports.
Unverified video posted online showed people marching in the city of Homs.
There were also reports of protests in the Kurdish city of Qamishli in Syria's north, and in the coastal towns of Latakia and Baniyas, which have seen regular marches in recent weeks.
The BBC's Jim Muir, in Lebanon, said two people were reportedly wounded in Latakia.
But the impression was the government was trying to avoid major bloodshed as the UN rights body held its meeting.
Ahead of the protests, a notice on the Facebook page Syrian Revolution 2011 called for a "Friday of Anger".
"To the youths of the revolution, tomorrow we will be in all the places, in all the streets," it said.
"We will gather at the besieged towns, including with our brothers in Deraa."
Protests were backed this week by the Muslim Brotherhood, the Islamist organisation crushed by President Assad's father in the 1980s and banned ever since.
"Do not let the regime besiege your compatriots," said the statement, thought to be the first direct appeal by the group.
"Chant with one voice for freedom and dignity. Do not allow the tyrant to enslave you."'Corpse clubbed'
In Deraa, at least 50 people are reported to have been shot dead in recent days.
Some bodies are still in the streets as snipers are said to be targeting anyone who tries to retrieve the dead.
Unverifiable video footage posted on the internet showed security forces clubbing a dead body in the street before dragging it away.
Witnesses said water, communications and power had been cut off.
Deraa is the southern city in which political protests began in Syria six weeks ago.
A military crackdown was launched there on Monday, with security forces backed by tanks forcing their way into the centre of the city.
Syrian authorities say they are acting to restore security.
Foreign journalists have been banned from Syria and reports from inside the country are difficult to verify.
There are unconfirmed reports of divisions within the security forces and of soldiers refusing orders to fire on protesters.
On Wednesday, 200 members of Syria's ruling Baath party resigned after issuing an angry public statement denouncing the repression.
The resignations - mostly from around Deraa - follow those of 30 Baath officials from the coastal city of Baniyas, north-west of Damascus.
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