The annual march to commemorate the fatal shooting of 15-year old Alexandros Grigoropoulos passed by parliament and ended near the Exarchia district where the unarmed boy was shot dead by a policeman. The gathering, which usually draws anti-establishment protesters, was largely peaceful.
After the march, hooded protesters threw petrol bombs at riot police, who launched teargas and flash bombs at the crowds. Similar violence broke out in the northern city of Thessaloniki after the annual demonstrations.
Hundreds of Greek students marched peacefully earlier in the day through central Athens.
Demonstrators chanting "Your hands off our bodies!" also protested over the police shooting of a 16-year old Roma boy on Monday, who is being treated at a hospital in Thessaloniki with head injuries.
Police alleged the boy filled up the truck he was driving with fuel and drove off a petrol station without paying. He was chased by police and one officer has been arrested over the boy's injury.
The incident has led to protests by Roma groups in both cities and clashes between police and protesters.
On Tuesday, more than 4,000 officers were deployed in central Athens. Some in full riot gear formed cordons outside parliament and businesses in central Athens. A police helicopter hovered over the city.
On the night of Dec. 6, 2008, hours after Grigoropoulos was shot, thousands took to the streets of Athens, torching cars and smashing window shops and looting. Two years later, the police officer was sentenced to life imprisonment but was later released by an Appeal's court.
The 2008 riots, which were also fuelled by anger over unemployment and economic hardship in a prelude to Greece's decade-long debt crisis, lasted for weeks.
(Reporting by Renee Maltezou and Alkis Konstantinidis; Editing by Aurora Ellis)
