Two goals from 17-year-old Charis Mavrias earned Greece their second win from three matches in UEFA European Under-21 Championship qualifying Group 1.
The Panathinaikos FC midfielder struck in each half against San Marino – his first goals at this level – at the Peristeri Stadium, and each time was set up by fellow teenager Kostas Fortounis.
Mattia Manzaroli had already saved San Marino on three occasions before the pressure finally told on 24 minutes when Mavrias collected Fortounis's through ball, rounded the goalkeeper and slotted in from a narrow angle.
Thanassis Karagounis struck the crossbar with a header ten minutes before half-time but a dominant Greece eventually doubled their lead just after the hour with Fortounis feeding Mavrias, who scored with a powerful drive.
Giorgos Georgiadis's charges face Belarus − who they were beaten 3-2 at home by in August − on Tuesday. San Marino, bottom of the group after a fourth successive defeat, host leaders Germany 24 hours earlier.
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