Vatican spokesman the Rev Federico Lombardi said their talks concentrated on the Ukraine conflict and the Middle East, where the Holy See is worried about the fate of the Christian minority.
Putin earlier today met Italian Prime Minister Matteo Renzi in Milan and arrived an hour late to the meeting at the Vatican, his second with Francis since he became pope in 2013.
Lombardi said Francis stressed the need "to commit oneself in a sincere and great effort to bring" peace to Ukraine, through dialogue and implementation of the Minsk accords.
The US ambassador to the Holy See, Kenneth Hackett, said the U.S. Would like to see the Vatican increase its concern about what is happening in Ukraine during the pope's meeting with Putin.
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"We think they could say something more about concern of territorial integrity, those types of issues," Hackett told reporters. "It does seem that Russia is supporting the insurgents. And it does seem that there are Russian troops inside Ukraine. This is a very serious situation."
Renzi greeted Putin as Russia's "dear" president and didn't voice any criticism against the country's actions in Ukraine, saying simply that they both agreed there must be full implementation of the Minsk peace accord.
Renzi met Putin after a tour of Russia's pavilion at Milan's Expo.
At a brief Russian-Italian news conference in Milan, Putin stressed the price Italian businesses are paying for the economic sanctions lodged by the European Union against Russia, which annexed Crimea from Ukraine during the conflict.