In the Russian capital's first mayoral election in a decade, Muscovites had to choose from six candidates including current pro-Kremlin mayor Sergei Sobyanin and main opposition candidate Alexei Navalny.
The candidacy of anti-corruption blogger Navalny has made the race the first genuinely competitive Russian election since the heady early post-Soviet years.
The vote will be seen as a crucial test of the protest mood in a city which was shaken by huge demonstrations against Putin's decade-long rule in the winter of 2011-2012.
Opinion polls indicate Kremlin-backed Sobyanin, 55, will win a majority in today's poll, while Navalny is set to come second with around 20 per cent.
The 37-year-old Navalny, who shot to prominence during the anti-Putin rallies, has earned comparisons to a young Boris Yeltsin, Russia's first post-Soviet president, for his exuberant energy, good looks and promise of change.
The four other candidates in the poll are: a representative of a Kremlin-friendly party, a Communist, an ultra-nationalist lawmaker and a liberal opposition figure.
The main intrigue in the upcoming polls is not how many vote for the pro-Kremlin incumbent but what happens to Navalny, who has been campaigning under the burden of a five-year prison sentence on what he says are trumped-up charges.
The blogger, who first made a name for himself exposing corruption among the elites, has vowed to jail Putin and his allies if he is one day elected president.
At the start of the campaign, Navalny was sentenced to five years in a penal colony on fraud charges and arrested in court.
Despite Navalny becoming an increasingly visible presence in Russia's politics, Putin still refuses to mention him by name and refers to him as "this gentleman."
The Russian president has made no secret of his support for his former chief of staff Sobyanin, however, praising him profusely in an interview ahead of the poll.
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