Chicago police said they responded to the incident in the 4100 block of West Chicago Avenue just after 11 a.m. Friday.
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The man who police believed was armed was seen on top of the building waving what appeared to be guns and a blow torch.
Video from Chopper 7HD showed the scaffolding the man was using to display an anti-Semitic sign, the Chicago flag, the Ukrainian flag, and an upside down American flag which is a universal sign of distress.
Police blocked traffic from a six-block radius around the incident.
In a statement issued early Saturday morning, police said after officers arrived, the man entered the building "and refused to exit the premises."
"SWAT officers made entry into the building and discovered a male adult deceased on scene," said police, who didn't say what time officers made entry and found the man.
SWAT responds to possibly armed man on warehouse roof on NW Side
Chantal Robinson was on edge as she picked her kids up from school Friday.
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"It is crazy. When they called me, I thought something had happened to them," she said.
The man was known to some residents of West Humboldt Park.
"If he likes you, he talks to your or whatever, he's the kind of guy that will give you the shirt off his back," said Gregory Wynne, neighbor.
"He's always playing anti-Semitic music," said resident Eric McNeil.
Frustrated residents and community groups said they have warned city officials and CPD about the dangerous situation, only to have it happen again.
"It's been three different times," said Titus Washington, who works in the neighborhood. "I've been working here eight months and on three different occasions they have this whole block cut off because of him."