No injuries or arrests were reported. About 3,000 anarchists, left-wing group supporters and students marched through the city center in a demonstration originally planned to reach the US Embassy in another part of town.
A second planned Athens protest by Communist party supporters was due to start later today.
All demonstrations have been banned in a large swathe of central Athens during Obama's two-day visit. Riot police blocked the marchers from the part of the city where Obama will be, parking buses across roads and manning cordons.
There is a strong anti-American tradition among Greek left-wingers who still resent U.S. Support for Greece's 1967-74 military dictatorship.
Obama's visit comes just two days before the country's main annual anti-American demonstrations, which commemorate the bloody suppression, by military authorities in 1973, of a pro-democracy student uprising.
The last visit to Greece by a US president was by Bill Clinton in 1999. It was marred by extensive street fighting between anarchists and riot police.
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