The rampage in the Jihad neighborhood was in apparent retaliation for the Saturday night car bombing of a Shiite mosque that killed two and wounded nine. Sunni leaders expressed outrage over the Sunday attacks, referring to them as a "massacre."
Armed men belonging to the Mahdi army, the Shiite militia loyal to radical cleric Muqtada al-Sadr, sealed off roads leading to the neighboring area of Shula, fearing reprisals, police said, although al-Sadr aides denied their militiamen were behind the attacks. Clashes also were reported in the area and in eastern Baghdad.
Two parked car bombs later struck the al-Timim Shiite mosque in central Baghdad, killing 17 people and wounding 38, according to police Lt. Mohammed Khayoun.
Police and witnesses said gunmen pulled up in four cars in the dangerous Jihad neighborhood in western Baghdad at about 10 a.m. and began seizing pedestrians and people in vehicles.
An Interior Ministry official, speaking on condition of anonymity for security reasons, said Shiite militiamen wearing masks and black uniforms roamed the neighborhood, abducting Sunnis.
Wissam Mohammad Hussein al-Ani, a 27-year-old Sunni calligrapher, said three gunmen stopped him as he walked toward the bus and asked him to produce his identification. They let him go after he produced a fake ID with a Shiite name but seized two young men standing nearby.
The Shiite owner of a supermarket in the area said he saw heavily armed men pull four people out of a car, blindfold them and force them to stand to the side while they grabbed five others out of a minivan.
"After ten minutes, the gunmen took the nine people to a place few meters away from the market and opened fire on them," Saad Jawad Kadhim al-Azzawi said. "When I heard the gunfire, I closed my supermarket and went home."
Police Lt. Maitham Abdul-Razzaq said 41 bodies were taken to hospitals and police were searching for more victims reportedly left dumped in the streets. He also said U.S. and Iraqi forces had sealed off the area.
Witnesses said the American forces were using loudspeakers to announce a two-day curfew.
Government leaders urged calm, with the prime minister's office saying the situation was under control and President Jalal Talabani calling on Iraqis to cling to national unity and "not be provoked by acts of violence that some want to look sectarian."
The cleric called for an emergency session of parliament to discuss the sectarian crisis and said he will form an investigative committee to bring those involved to justice, even if they are part of his Mahdi Army militia, al-Hashimi's secretary said.
But Sunnis were irate. Deputy Prime Minister Salam al-Zubaie, a member of the sect, called the attack "a real and ugly massacre," and blamed Iraqi security forces, widely believed to have been infiltrated by Shiite militias, for failing to maintain order.
"There are officers who instead of being in charge should be questioned and referred to judicial authorities," al-Zubaie told Al-Jazeera TV. "Jihad is witnessing a catastrophic crime."
Prime Minister Nouri al-Maliki's office distanced itself from al-Zubaie's comments, issuing a statement saying they "do not represent the government's point of view."
The Shiite-led government has vowed to crack down on Shiite militias and Iraqi troops backed by U.S. jets raided the stronghold of Sadr City on Friday, killing and wounding dozens of people.
An Interior Ministry aide said the situation was brought under control after several hours.
Maj. Gen. Ali Jasim told The Associated Press that by mid-afternoon, the neighborhood was "under the full control" of Interior Ministry commandos.
Alaa Maki, a member of the largest Sunni bloc in parliament, accused Shiite extremists of trying to wipe out the minority, which was dominant under Saddam Hussein but lost power to majority Shiites after his ouster.
"We demand the presidency, the prime minister and the parliament stand against this agenda," he said. "The situation is very serious. If it deteriorates, all of us will be losers."
Some Sunni leaders blamed the Madhdi army.
Sheikh Abdul Samad al-Hadithi, imam of the Fakhri Shanshal Sunni mosque that also was hit by a car bomb Friday, with two people killed, said the militiamen were looking for revenge for the bombing against the Shiite mosque Saturday.
He said they first set up checkpoints and killed nine employees of the Sunni Endowment, the state agency responsible for Sunni mosques and shrines, then went on a rampage, killing more than 50 people according to their IDs.
"They wanted to retaliate against people of the other sect," al-Hadithi said, accusing Interior Ministry forces at the site of standing by while the attacks occurred.
Al-Sadr aide Sheik Abdul-Hadi al-Darraji denied any links, saying the attackers were wearing the black uniforms to provoke sectarian tension.
Clashes also broke out between gunmen and Iraqi police in the eastern Fadhal neighborhood, but the situation was brought under control after several hours, Abdul-Razzaq said.
In other violence, gunmen killed an Iraqi intelligence officer in the Shiite holy city of Karbala, one of several deadly shootings targeting security forces.
The officer was gunned down after his car was intercepted in the center of Karbala, 50 miles south of Baghdad, health official Salim al-Abadi said.
Gunmen also opened fire on a foot patrol in eastern Baghdad, killing a policeman, police said. Another policeman was killed in a drive-by shooting in the northern city of Kirkuk.