They were arrested in a raid Wednesday night, but formally charged Saturday as heads of state began arriving in the city for the NATO summit.
The three are Brian Church, 27, of Fort Lauderdale, Fla.; Jared Chase, 24, of Keene, N.H. and Brent Vincent Betterly, 24, the Chicago Sun-Times reported. Betterly told police he lived in Massachusetts.
They were charged in state court with possession of an explosive or incendiary device, conspiracy to commit terrorism and providing material support to terrorism.
The Sun-Times said Chicago undercover police had infiltrated a group of NATO summit protesters and observed them as they made Molotov cocktails.
Britain's The Guardian newspaper said the investigation took a month.
Each of the three was being held on a $1.5 million bond, The Guardian said.
Lawyers representing the men said the charges are trumped up to intimidate protesters.
"We cannot say enough that we believe that these charges are absolutely … very trumped up charges," Sarah Gelsomino of the Peoples Law Office said, The Guardian reported. "Clearly in an attempt to continue this intimidation campaign on activists. Charging these people who are here to peacefully protest against NATO for terrorism, when in reality the police have been terrorizing activists in Chicago, is absolutely outrageous."
Protesters and Chicago police engaged in several pushing and shoving incidents Saturday, with police detaining some protesters but permitting a march to go on, as a crowd of protesters in the Loop grew from about 300 earlier in the day to several times that number Saturday evening, the Chicago Tribune reported.
Anti-NATO protesters disrupted traffic in downtown Chicago Friday following the first official demonstration tied to the NATO summit.
Police, some in riot gear, arrested at least one demonstrator on the Michigan Avenue Bridge after protesters swarmed the area, blocking traffic. One demonstrator was caught on video by WLS-TV, Chicago, tearing down one of the NATO welcoming signs on a bridge tower.
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