user: Article: "We will need to teach the president-elect what Europe is and how it works," Mr Juncker told students in Luxembourg.
The Commission chief predicted that two years would be wasted while Mr Trump "tours a world he doesn't know".
His remarks contrasted with other EU leaders' more muted reaction to the Tuesday's shock election result.
American cities have seen angry protests since Mr Trump's election victory over the Democratic candidate, Hillary Clinton.
In New York, Mr Trump set about forming the team that will see him through to his inauguration on 20 January, when he replaces Barack Obama in the White House.
Mr Juncker had offered his formal congratulations to Mr Trump on Wednesday in a joint statement with Donald Tusk, head of the European Council.
Speaking on Friday, he said: "In general the Americans take no interest in Europe...
"During the campaign, Mr Trump said Belgium was a village somewhere on our continent...
"He raises questions which could have harmful consequences because he calls into question the trans-Atlantic alliance, and thus the model on which Europe's defence rests.
"He takes a view of refugees and non-white Americans which does not reflect European convictions and feelings."
During the election campaign, Mr Trump caused alarm in EU circles with his sharp criticism of Nato, the cornerstone of Western Europe's defence structure, and calls for better relations with Russia.
His promise to "cancel" the Paris Climate Agreement within 100 days of taking office and protectionist stance on trade have also caused concern, as have his controversial comments about ethnic and religious minorities.
While EU leaders congratulated the Republican on his shock victory over Hillary Clinton, German Chancellor Angela Merkel stressed in her message to him that the US and Germany shared "the values of democracy, freedom, respect for the rule of law and human dignity, regardless of origin, skin colour, religion, gender, sexual orientation or political belief".
Germany, France and the Netherlands all face elections in the new year, with populist and far-right parties poised to capitalise on discontent with the EU's continuing migrant problem and its slow recovery from the eurozone debt crisis.
Before Mr Trump's victory, the EU had already been rocked by the UK's vote to leave the body at a referendum in June.
However, on Thursday, UK Foreign Secretary Boris Johnson urged his EU colleagues to take a more positive attitude.
"I would respectfully say to my beloved European friends and colleagues that it's time that we snapped out of the general doom and gloom about the result of this election," he said on a visit to Serbia.
Meanwhile, in New York, outgoing UN Secretary General Ban Ki-moon said he was confident Mr Trump would not rip up the Paris agreement on climate change, despite his campaign pledge.
"He has made a lot of worrying statements but I am sure that he will understand the whole importance and seriousness and urgency," he told AFP news agency.
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Summarize: Donald Trump's election risks upsetting EU ties with the US "fundamentally and structurally", EU Commission President Jean-Claude Juncker has warned.


Article: The injured man is in a critical condition in hospital after being found at about 22:50 BST on Monday in a flat in Rochester Street, Chatham.
Another man in his 60s, who police believe may be connected to the attack, was found in Pagitt Street and is being treated for a head injury.
The 62-year-old man was arrested on suspicion of murder and is in custody.
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Summarize: A 62-year-old man has been arrested after a man in his 30s was found seriously injured with stab wounds.


Article: Alan McBain, 60, died and his 58-year-old wife was badly injured in the incident close to Dalmeny on Monday.
They were both on an unclassified road between the B800 and Standingstane Road when they were hit by a blue Mini.
Police Scotland said Mrs McBain remained in a serious condition in hospital, and appealed for witnesses to come forward.
Con Denise Humphrey said: "Our sincere condolences go to Alan's family and friends at this very sad time.
"We are still keen to speak to anyone who witnessed the collision or who has information that can assist us with our investigation.
"Anyone who hasn't so far contacted us is asked to call 101 to speak to a road policing officer."
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Summarize: A pedestrian who died after he was hit by a car near Edinburgh has been named by police.


Article: Commuters have been using the route under the M74, at the Raith Interchange on the A725 between Bellshill and East Kilbride, for the first time.
Transport Scotland said the roundabout had struggled to cope with 75,000 vehicles using the junction each day.
Work is still underway on other parts of the Â£500m motorway improvement plan which began in February 2014.
Commuting traffic was still slow on the M74 southbound between junction 2 and the Raith Interchange at junction 5, with travel times of about 45 minutes in the roadwork area at about 09:30.
Scottish Roads Partnership (SRP) is upgrading the A8 between Glasgow and Edinburgh and making major improvements to the M73, M74 and A725.
Now, 50 years after the Raith junction first opened to traffic, SRP have also constructed three new bridges to carry the motorway and local traffic over the new underpass.
In addition, two new footbridges are being installed over the roundabout which will create a safe access route over the busy junction between Bothwell and Strathclyde Country Park.
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Summarize:

assistant: A new underpass has opened below a heavily-congested roundabout near Hamilton in South Lanarkshire.