The storms moved through Madison, Wisconsin about 1 a.m., moving south at 50 mph, ABC7 Meteorologist Larry Mowry said. There were tornado warnings with the storm near Madison, he said.
The Illinois Department of Transportation reported some trees down in Waukegan just before 4 a.m., as a result of the storms.
In north suburban Zion, the storms came with a lot of lightning, heavy rain and some high winds.
Near Zion Middle School, a few very large tree branches were blocking 27th Street. Some power lines appeared to be affected, too.
Some residents said they thought a tornado was coming through, so when part of a tree fell on their roof, they ran to the basement.
To their surprise, it wasn't a tornado -- instead, a quick moving wicked storm.
In Chicago, siding from a two-story warehouse appeared to have been ripped off a Galewood building and tossed onto the Metra tracks, affecting the Metra Milwaukee District West.
Meg Reile, a Metra spokeswoman, said trains are not currently traveling past Bensenville on the line. In addition to the siding, there are wires across the tracks, she said.
WATCH: Chicago storm damage disrupts Metra service
There was not immediately an estimate of how soon service would resume.
And in Park Ridge, the winds were so strong, a huge part of the trunk splintered off an old oak tree, landing on top of a home, crushing the chimney and two cars in the driveway.
In Skokie, a large tree came down, blocking the ramp to the Edens at Old Orchard Road.
At the storm's height, ComEd said over 40,000 customers were without power.