The Quds (Jerusalem) Day rallies - founded in Iran after the Islamic revolution in 1979 - show support for Palestinians and opposition to Israel.
But supporters of opposition leaders, including Mir-Hossein Mousavi, used this year's marches as a rallying point for their cause.
It was the first time in two months that opponents of President Mahmoud Ahmadinejad had taken to the streets following a government crackdown.
Pro-reform leader Mehdi Karroubi joined the protests and was cheered by his supporters.
Meanwhile, bodyguards of reformist former President Mohammad Khatami had to protect him from angry hardliners during the rally in Tehran.
Protesters were caught up in clashes with security forces and witnesses say there were several arrests.
Some opposition supporters burned a Russian flag in protest at President Ahmadinejad's close ties with Moscow.
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