The marchers carried flags and banners saying "No to occupation" and demanding that the unity of Iraq be preserved.
A BBC correspondent at the scene says it is the biggest demonstration of Arab nationalism since the end of the war, and shows what powerful sentiments the US-led invasion of Iraq has stirred up.
The protesters were led by a respected and well-known Sunni Muslim scholar, Ahmed al-Kubaisi.
He is reported to have used his sermon to denounce the American-led invasion, whose purpose, he said, was to defend Israel.
Our correspondent says there was a tense confrontation earlier when an American patrol stumbled into a crowd kneeling outside a mosque.
He says the worshippers surged forward angrily, but the US commander skilfully withdrew his troops and defused the situation.
The troops had entered the area of the mosque to distribute humanitarian aid.
It was the first full Friday prayers since Baghdad fell to US-led forces last week.
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