The troops searched several sites in Sadr City -- an impoverished district controlled by Shia gunmen, where US commanders fear an abducted soldier is being held -- according to residents and an Iraqi defence official.
Previous raids into the volatile area have provoked violent clashes and revealed divisions between US commanders and Prime Minister Nuri al-Maliki's government, but Friday's operation appeared to be proceeding peacefully.
"Iraqi and coalition forces continue to conduct operations in order to recover the missing soldier," said US military spokesman Lieutenant Colonel Chris Garver, when asked about the operation in Sadr City.
"Due to operational concerns, we can't talk about ongoing operations," he added, as US helicopters could be seen flying over the area and plumes of smoke rose over the city skyline.
According to an Iraqi defence official there was a brief exchange of fire between US troops and radical cleric Moqtada al-Sadr's Mahdi Army militia, but there were no casualties and the gunmen dispersed when helicopters arrived.
American forces and an Iraqi special forces unit searched homes, a school and the offices of a mosque controlled by Sadr's movement, he added.
"They came into the Imam Ali mosque while it was empty, as the faithful were praying outside Sadr's office next door," the mosque's muezzin, Hamza Rikabi, told AFP at the scene, once the US-led force had moved on.
"They checked one of our computers and stayed for about half-an-hour while they searched a nearby school and some houses," he added.
While the US troops were searching the suburb a mortar shell hit the headquarters of Iraqi state television five kilometres (three miles) away in western Baghdad, wounding two guards, a station employee told AFP.
Shia militia often respond with mortar fire against mainly Sunni west Baghdad when US forces move against them in the east.
On Monday, an American soldier of Iraqi descent slipped away from his base inside Baghdad's fortified Green Zone in order to visit Iraqi relatives in the city, according to US military spokesmen.
His family later reported that masked gunmen had abducted him from their home, triggering a massive manhunt that brought thousands of US forces onto the streets, where they set up checkpoints on roads into Sadr City.
On Wednesday, US and Iraqi forces conducted pre-dawn raids on two Sadr City addresses and called in an air strike after triggering a violent clash with local gunmen. At least 10 militants and four civilians were killed.
Maliki was fiercely critical of the raid, underlining the tense relations between Washington and its main Iraqi ally as both countries' forces struggle to contain a bloody wave of sectarian violence.
On Friday, the first day of prayers after the Eid al-Fitr holiday was relatively peaceful.
Police found the bodies of 11 murder victims on Thursday and overnight, a US military spokeswoman said, a toll considered low by the standards of Baghdad's vicious war between rival Sunni and Shia death squads.
Meanwhile, with US casualties for the month so far running at their highest level in a year and 24 Iraqi police killed in an insurgent ambush on Thursday, the Al Qaeda militant group issued a triumphant statement.
"We call on all mujahideen... to support the young Islamic state in Iraq. Weakness has gripped the infidel nations. The first signs of victory can be seen on the horizon," the group said in an Internet statement.
The message, which could not be independently authenticated, was issued in the name of the self-proclaimed Islamic Emirate of Iraq, which was declared on October 15 by a Qaeda-led coalition of insurgent groups.
It coincided with fierce fighting between Al Qaeda and US forces in the western Iraqi city of Ramadi, in the heartland of the Sunni rebellion, where at least five American sailors and marines were killed on Wednesday.
Last month's declaration of the emirate was marked by a brief show of force by insurgents, filmed by televisions crews, driving cars full of armed militants through central Ramadi bearing Al Qaeda banners.
The US-led coalition has denied losing control of the situation, but on Thursday military spokesman General William Caldwell said the marines based in Ramadi were engaged in a tough operation to "take back" the city.
"They're continuing to have progress. They, in co-ordination with Iraqi security forces, are on a daily conflict with the insurgent elements out there, but they are in fact moving forward," he told reporters on Thursday.
"They're doing it very aggressively out there... And it's an aggressive offensive approach to taking back the city of Ramadi, to return it back to Iraqi security force control," he said.

Copyright AFP (Agence France-Presse), 2006