He placed a bouquet on a pile of flowers, balloons and other commemorative items that has risen at the site of the trolleybus bombing in Volgograd, and then visited a hospital in the city where some of the wounded are being treated.
A total of 34 people were killed and about 60 people were injured in the two suicide attacks. The other attack was committed at a railway station.
Mr Putin's pre-dawn visit came after he pledged on state TV to annihilate those responsible as security is stepped up prior to the Winter Olympics in Sochi, which will begin next month.
"No matter what motivated the criminals, there can be no justification for crimes against civilians, particularly against women and children," Mr Putin said.
"The vileness of the crime - or crimes - that were committed here, in Volgograd, needs no additional commentary."
Islamist insurgents in the North Caucasus have plagued Mr Putin's 14-year rule.
A suicide bomb blast in Volgograd's main railway station on Sunday afternoon killed at least 18 people, and a second attacker blew up a trolley bus in rush hour on Monday morning, killing 16 and leaving bodies strewn on the street.