The U.S. military reported that some 100 guerrillas were killed and nearly 200 other people were wounded in hours of fierce street fighting and air strikes.
A doctor at the town's main hospital said at least 21 civilians were killed and 35 wounded in the clashes.
The assault began shortly after midnight with a series of air strikes and artillery barrages pounding targets in the town. The rebels fought back with rocket-propelled grenades and mortars.
The U.S. military said two U.S. soldiers were wounded during the operation in the city, around 100 kilometers north of Baghdad. They said troops destroyed many mortar sites, rocket-propelled grenade teams and vehicles used to carry insurgents.
The U.S. military also reported Iraqi commandos had taken control of Samarra's Shi'ite Golden Mosque and captured some 25 insurgents inside the building.
To the south, in Kufa, Iraqi security forces prevented hundreds of Shi'ite Muslim supporters of cleric Muqtada al-Sadr from entering the city's main mosque for prayers. Police fired into the air to disperse worshippers, who left shouting slogans in support of al-Sadr.
The U.S. military said it will retake control of guerrilla strongholds like Samarra, the western cities of Al-Fallujah and Ramadi, and the Baghdad districts of Al-Sadr City and Haifa Street by the end of the year so elections can go ahead in January.
The operation in Samarra came one day after at least 46 people were killed and more than 200 wounded in a series of car bombings around Iraq's capital.
(Reuters/dpa/AP)For the latest news on Iraq, see RFE/RL's webpage on "The New Iraq".