Putin made no statement as he strode in and posed briefly for photographers with interlocutors, European Council president Herman Van Rompuy and European Commission head Jose Manuel Barroso.
There was little security in place around EU headquarters and shortly before Putin's arrival, Belgian police detained two bare-breasted Femen activists protesting against the Russian leader.
"Putin, Killer of Democracy" was scrawled across the torso of one while the other sported a Stalin-style moustache and the words "Good Job Putin".
"We need to clear the air" with Russia, a senior EU official said, after Moscow in November pressured Ukraine into dropping a trade and political deal meant to be the centrepiece of the EU's much vaunted Eastern Partnership strategy -- tightening relations in the region on the basis of shared democratic values.
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"We could not simply have a business-as-usual summit," the EU official said, adding there had to be some "straight talking... A strategic, fundamental discussion" of the EU-Russia relationship.
Today's summit was shortened to just under three hours after a dinner yesterday was dropped.
Putin, van Rompuy and Barroso will be joined by EU foreign affairs head Catherine Ashton and Russian Foreign Minister Sergei Lavrov, plus a strict minimum of aides, EU officials said.