As Mr Clinton, his wife Hillary and their daughter Chelsea walked away from their plane, hundreds of police in riot gear and gas masks fired several rounds of teargas at the protesters.
"I have come here as a `philhellene' - a friend of Greece, and I look forward to experiencing that wonderful quality of Greek hospitality known to all the world," Mr Clinton declared shortly after his arrival.
But his presence provoked running street battles as the demonstrators, many of them venting their anger at the Nato bombing of Yugoslavia, set up barricades and lit fires in parts of central Syndagma Square. Many shops and at least four banks were on fire.
The tone of the chants and slogans was anything but hospitable. "Let's all join together to give the murderer the reception he deserves, all together for the big march to the embassy," a voice blared from a loudspeaker in Syndagma.
Two giant banners scrawled with the words "Killer Clinton" had been erected on a mountainside overlooking central Athens. An American flag defaced with a large swastika was draped across a building across from Mr Clinton's hotel.
The President arrived in Greece amid heightened fears that he could be the target of extreme left wing Greek terrorists. Some 3,000 FBI agents and counter terrorism experts were rumoured to be in Athens. Most of the concern was focused on the Marxist-Leninist revolutionary organisation "November 17". In the past 25 years, the underground group has assassinated four US diplomats and tried to kill hundreds more.
Greek police refused permission yesterday for a march on the American embassy but left wing groups and the Communist party urged demonstrators to defy the ruling and proceed to that area anyway.
Earlier, Mr Clinton said he was not worried about the demonstrations. "I'm delighted to be going and I'm not concerned about the protests. Greece is the world's oldest democracy. If people want to protest they should have a chance to do it."
Athens announced last week that the Clinton visit, originally scheduled to run from 13 to 15 November, was being postponed and cut from three days because of fears for his safety in the run up to 17 November, the anniversary of a 1973 crackdown on a student uprising against the military dictatorship of the day. Many Greeks still blame the US for its support of the colonels and 17 November is traditionally a day of anti- US rallies.
Security was stepped up after four gas-canister bombs exploded outside a local car dealer as protests grew against the visit and American targets were attacked in three other incidents. Protests in recent days have seen Mr Clinton compared to Adolf Hitler and tried in a mock court on Athens main square as "the butcher of the Balkans".
The trip to Greece had been scheduled to kick off a 10 day Clinton tour aimed at advancing reconciliation between Greece and Turkey.