Iran's Supreme Leader, Ayatollah Ali Khamenei, has sought to calm tensions and called for an end to rioting.
The authorities have also promised a recount of the disputed votes - but the opposition demands a full rerun.
Heavy restrictions have been placed on the BBC and other foreign news organisations. Reporters are not allowed to cover unauthorised gatherings or move around freely in Tehran - but there are no controls over what they can write or say.
Opposition demonstrations gathered in force in central Tehran on Wednesday afternoon.
Jon Leyne, BBC News, Tehran
The opposition is keeping up the pressure.
On the other side I get the impression the government hasn't really worked out a comprehensive response, instead they're sort of harassing the opposition.
There have been more arrests of opposition figures - not the most senior leaders, but still pretty well-known names. They've been sending in their thugs, basically, their militia, to attack student dormitories, and they've been arresting journalists.
At the moment, there's absolutely no sign of loss of momentum, in fact it's building.
What this election result has unleashed is just a deep frustration, an anger that I've certainly sensed in the two years I've lived here. People are so frustrated and angry with the system, which seems to treat them with contempt.
The BBC's Jon Leyne in the capital says it is difficult to verify the numbers attending. Some estimates say between 70,000 and 100,000, others up to 500,000.
The march, from Haft-e Tir square to Vali Asr square, was reported to be in silence to try to avoid provoking the authorities.
Many people wore green - the colour used by Mr Mousavi in his election campaign - and black, in memory of the protesters killed. The demonstrators also carried placards alleging election fraud.
Iranian state television has aired brief footage of the rally.
Our correspondent says the picture outside Tehran is more confused but there are reports of demonstrations and government attacks on demonstrations.
He adds that there could be another real push by the opposition on Thursday.
Mr Mousavi has called for a day of mourning to be held then in memory of those killed. He has also called for a mass demonstration and for protesters to again wear or carry black.
"We are after a peaceful rally to protest the unhealthy trend of the elections and realise our goal of annulling the election results," Mr Mousavi said in a statement on his website reported by the Associated Press.
He said he was seeking a new election that would not repeat the "shameful fraud" of last week's vote.
Our correspondent says that the government may try to draw protesters into a confrontation in order to discredit them.
In other developments on Wednesday:
• Six footballers playing for Iran's national team, including the captain, have appeared in a World Cup qualifier in Seoul, South Korea, wearing armbands in the green associated with Mr Mousavi
Footage of the Iranian team members wearing the wristbands
• The Iranian government summoned the Swiss ambassador - who represents US interests in Iran - to complain at Washington's "interventionist approach" on the election issue. The White House denied the charge
• Two pro-reform figures, newspaper editor Saeed Laylaz and Hamid Reza Jalaipour, an activist and journalist, were arrested on Wednesday morning, reports said. Mr Laylaz is a political and economic analyst who is often critical of Mr Ahmadinejad and who has often been interviewed by foreign media.
Overnight, members of Iran's Basij volunteer militia reportedly raided university dormitories in several Iranian cities.
The Basijis stormed compounds, ransacking dormitories and beating up some students. Several arrests were made, our correspondent says, and the dean of the university in the city of Shiraz has resigned.
Students have been active among Iran's opposition and there have been several reports of security forces moving in on university premises since protests began over the weekend.
In the most high-profile incident, 120 lecturers at Tehran university resigned after a raid on that institution.
The overnight raids came after another direct intervention in the crisis by Iran's Supreme Leader Ayatollah Ali Khamenei.
Nobody should take any action that would create tension, and all have to explicitly say they are against tension and riots
Ayatollah Khamenei has not appeared in public since the election results, but now seems to be deeply involved in the search for a solution to the stand-off.
Meeting representatives of the four election candidates, he urged all parties not to agitate their supporters and stir up an already tense situation. He also repeated his offer of a partial vote recount, a proposal already rejected by the main opposition.
"In the elections, voters had different tendencies, but they equally believe in the ruling system and support the Islamic Republic," the Associated Press reported him as saying.
"Nobody should take any action that would create tension, and all have to explicitly say they are against tension and riots."
Are you in Iran? What do you think of the current situation? If you have any information you would like to share with the BBC you can do so using the form below:
Send your pictures and video to firstname.lastname@example.org or text them to +44 7725 100 100. If you have a large file you can upload here.
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.