The opposition says the protest – on an island just south of the Kremlin – could become the largest the country has seen in two decades.
Smaller rallies have taken place in cities across the country.
Hundreds of people have been arrested during anti-Putin protests over the past week, mainly in Moscow and St Petersburg.
At least 50,000 police and riot troops were deployed in Moscow ahead of Saturday’s protests.
Authorities have permitted up to 30,000 to attend the demonstration dubbed “For Fair Elections”.
Thousands have turned out for rallies in cities across the Urals and Siberia and as Far East as Vladivostok.
According to police, at least 25,000 people – among them communists, nationalists and liberals – have so far thronged in Moscow, and more crowds are heading towards the rally.
In Moscow, the two sides reached a deal by which authorities would allow a high turnout if the rally was relocated from central Revolution Square to Bolotnaya Square, a narrow island in the Moscow River where access points can be easily controlled.
Hundreds of police are standing by to make sure they do not rally in Revolution Square, though Reuters news agency said hundreds of people had gathered there anyway.
“This is history in the making for Russia,” Reuters quoted a 41-year-old employee in the financial services sector, who gave his name only as Anton, as saying at Revolution Square.
“The people are coming out to demand justice for the first time in two decades, justice in the elections.”
If the protests come even close to expectations, they will shake the 12-year-long political domination of Prime Minister Vladimir Putin.
The authorities permitted demonstrations to take place in specific locations in certain cities after negotiations with opposition leaders.
In St. Petersburg, 13,000 people have pledged on the social networking site Vkontakte to take part in protests, with another 20,000 saying they might take part.
Authorities have granted permission for a demonstration in one location, but say protests anywhere else will be illegal and will be dealt with.
Earlier in Vladivostok, seven time zones to the east of Moscow, several hundred people marched. At least 20 people were detained following a protest in the far-eastern city of Khabarovsk, local news agencies said.
But there is a widespread view, fuelled by mobile phone videos and accounts on internet social networking sites, that there was wholesale election fraud and that Vladimir Putin’s party cheated its way to victory.
On Friday, the presidential Council for Human Rights advising President Dmitry Medvedev said the reports of vote-rigging were of deep concern, and that the elections should be rerun if they were confirmed.
However the council has no power to order a fresh ballot.
Earlier this week, security experts said attempts had been made to counter online dissent in Russia, with hijacked PCs being used to drown out online chat on Twitter.
Analysis of the many pro-Kremlin messages posted to some discussions suggested they were sent by machines, according to security firm Trend Micro.
These are the most significant street protests against Vladimir Putin since he took power, but at this point they are not drawing the big numbers they would need to really put the Kremlin in trouble.
It will be a question of seeing whether the momentum builds and spreads from the metropolitan middle classes.
Even so, our correspondent adds, it is an extraordinary thing to witness Vladimir Putin under fire like this.
Vladimir Putin, who was president between 2000 and 2008, remains widely predicted to win a presidential election in March.
On Thursday, Vladimir Putin blamed the US for stoking the recent unrest, after Secretary of State Hilary Clinton expressed reservations over the poll.
The prime minister said Hilary Clinton’s remarks had “set the tone for some opposition activists”.
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