There has been an upsurge in fighting between US-led coalition forces and Shia militia in the Iraqi holy city of Najaf and nearby Kufa.
Najaf is home to the Imam Ali shrine
The US military said 32 fighters loyal to radical Shia cleric Moqtada Sadr were killed in a battle in the compound of a Kufa mosque on Saturday night.
Residents say US aircraft and artillery pounded the area before troops, backed by tanks, moved in.
In Najaf, there was heavy shelling around the vast, ancient cemetery.
Officials at a hospital in the city said 14 Iraqis were killed in the attack.
On Saturday, Moqtada Sadr's militia offered to withdraw from both Najaf and Karbala, but only if US troops pulled back as well.
Many members of Mr Sadr's Mehdi Army are reported to have quit the centre of Karbala, where they have been involved in heavy fighting with US-led forces for the last month.
Eyewitnesses said they have been returning to their homes and that the city is now calm.
Scenes of destruction
Pools of blood and tank tracks covered the floor of the Sahla mosque in Kufa after the battle between coalition troops and militia.
The US military said 12 rocket-propelled grenades and more than 200 mortar rounds were later found in the mosque compound.
Witnesses said hundreds of ground troops, backed by aerial support and tanks, were involved in the assault on the compound, which took place at 0100 on Sunday (2100 GMT on Saturday).
"Tanks crashed through the gates of the mosque compound during the night and soldiers entered while helicopters hovered overhead," Hussein Yasser, who lives near the mosque, told AFP.
Many local residents have been outraged that a religious shrine was attacked.
"I feel humiliated," Ali Wasi, one of about 100 residents who gathered at the site in the morning to protest, told Reuters.
"Our sanctity has been violated. These houses of prayer are the most valuable things we own, for Shias. I will resist them until the last drop of blood in my body," he said.
The mosque is 1.5km (one mile) from Kufa's main shrine, which Mr Sadr regularly visits to deliver Friday prayers.
US aircraft also carried out overnight airstrikes in Najaf, bombarding an area just to the north of the city's massive cemetery, where militants have holed up.
Local doctors said there were a number of civilians among the people killed there, along with some police officers caught when Najaf's main police station was hit.
In contrast, calm has returned to the streets of Karbala, after militia loyal to Mr Sadr began to withdraw.
A senior member of Mr Sadr's Mehdi Army, Ali al-Kazali, told the AFP news agency that the fighters had laid down their arms, following weeks of efforts by Iraqi tribal and religious leaders to negotiate a truce with the militia.
But Brig Gen Mark Kimmit denied any reports of a truce.
He repeated that the confrontation could only be resolved peacefully if Mr Sadr handed himself in and disbanded his army.
The US-led coalition has refused to negotiate directly with Mr Sadr, who is wanted in connection with the murder of a rival Shia cleric last year.