Putin's most vocal critic Alexei Navalny was also arrested
Dozens of protesters were held in the centre of St Petersburg, and more than 50 others were arrested by riot police near Pushkin Square in Moscow.
As demonstrators were taken away, hundreds of others shouted slogans such as "Putin is a thief" and "Shame!". Police in Moscow had gas masks and witnesses say pepper spray was used.
Russia's most prominent opposition leader Alexei Navalny was also arrested outside his home in Moscow earlier today.
Mr Navalny angered officials in Moscow after he made a last-minute decision to change the main protest's location to one of the city's busiest thoroughfares.
Police say he is going to be charged with failure to follow police orders and could be sent to jail for 15 days.
The 41-year-old had called for mass protests nationwide against corruption, with anti-graft demonstrations planned in more than 180 towns and cities.
Before the protest began on Tverskaya Street, a stone's throw away from the Kremlin, prosecutors warned the rally was illegal and police would take "all necessary measures" to prevent disorder.
Navalny is mounting a bid to unseat Mr Putin in next year's election, but polls suggest he has little chance of being successful because of the president's high ratings.
On his blog last week, he wrote: "I want changes. I want to live in a modern democratic state and I want our taxes to be converted into roads, schools and hospitals, not into yachts, palaces and vineyards."