Alexandros Grigoropoulos, 15, had been out with friends in a central Athens neighbourhood when he was shot on Dec 6, 2008 following a verbal altercation with police. His death led to two weeks of the most violent rioting Greece had seen in decades.
This year's anniversary marches come at a time when nearly nightly violent protests are being held by supporters of one of Grigoropoulos' friends, jailed anarchist and convicted bank robber Nikos Romanos, 21. He was present when Grigoropoulos was killed, is on a hunger strike, demanding prison leave to attend lectures after he passed university entrance exams.
Prime Minister Antonis Samaras will meet with Romanos' parents on Monday morning, following a request made through their lawyer, the government said.
Protesters during the demonstration chanted slogans in support of Romanos as well as in memory of Grigoropoulos.
In Thessaloniki, groups of youths broke off from a march of about 6,000 people, throwing Molotov cocktails and scuffling with police who responded with tear gas and stun grenades.