The vast gathering was part of nationwide protests in at least 15 cities across eight time zones after the Prime Minister's party was declared the winner of recent elections.
Former PM Mikhail Kasyanov - whose opposition movement was barred from the elections - was among those gathered in Bolotnaya Square near the Kremlin.
He declared: "Today 60,000, maybe 100,000 people, were at this rally.
"This means today is the beginning of the end for these thieving authorities."
Some believe the protests could become part of a Slavic Spring ? similar to the Arab Spring which toppled a string of unpopular regimes around the Middle East.
Protesters are demanding a re-run of last Sunday's disputed election and freedom for those arrested in previous protests this week.
Putin's United Russia party won but suffered a collapse in support according to the published results which showed a 20 per cent drop in vote despite widespread claims of "ballot-stuffing".
It had held two-thirds of the parliament's seats.
Demonstrator Alexander Trofimov said today: "The falsifications that authorities are doing today have turned the country into a big theatre, with clowns like in a circus."
Thousands of miles away in Vladivostok, several hundred protesters gathered shouting slogans including "Putin's a louse".
The protest in Moscow had received permission from the police but 15 people were arrested at an unauthorised protest in the Siberian city of Perm and a further 30 detained in the Far Eastern city of Khabarovsk.
In Kurgan, east of Moscow on Russia's border with Kazakhstan, an unsanctioned protest of about 400 people was dispersed.
There have been signs of a softer approach from Putin and Russian president Dmitry Medvedev who conceded election law may have been violated.
Many Russians felt disenfranchised when he and Putin announced plans to swap jobs after next year's presidential election and said they had taken the decision years ago.
Putin has suggested "dialogue with the opposition-minded" in the face of calls from US Secretary of State Hillary Clinton for a probe into alleged election fraud.