Passengers were hurled into the seats in front of them in the accident on the city's South Side, and four people had to be pulled from the front of the train, where the engine was located, authorities said.
The collision sent 71 people to a dozen hospitals, most of them in stable or good condition, according to the Chicago Fire Department. Five people were taken from the scene in serious to critical condition.
Fire Department spokeswoman Eve Rodriguez, speaking to CBS Station WBBM, confirmed a report that a conductor had been pinned inside.
The cause of the wreck was not immediately known.
The damage to the passenger train was mostly to its engine, where some of the five Amtrak workers aboard were, authorities said. It was unclear how many of them were hurt. The train's three double-decker passenger cars remained upright.
No one was in the portion of the Norfolk Southern freight train that was struck, and neither of the two workers aboard was hurt.
Amtrak passengers, many of them carrying winter coats and luggage, streamed off the train with the help of rescue workers. Some held the hands of children; others were taken away on stretchers and backboards.
Coert Vanderhill, 60, of Holland, Mich., said the train was approaching the station at 15 to 20 mph when the engine "just ran right up the tail end" of the freight train.
"Everybody just hit the seat in front of them," he said.
Vanderhill, who had come to Chicago to visit his children, had a small cut on his nose and said most of the other passengers also had minor injuries.
University of Chicago Medical Center got 13 patients, three of them in serious to critical condition, spokesman John Easton said. He said none of the patients had injuries that appeared to be life-threatening and he expected most people to be treated and released.
Cook County's Stroger Hospital was caring for another 25 patients, all with minor injuries, spokesman Sean Howard said. At Advocate Christ Medical Center, spokeswoman Deb Song said six of the 10 patients there were to be treated and released, and the rest were in fair or stable condition.
The Amtrak train was en route from Grand Rapids, Mich., to Chicago. The freight train was traveling from Elizabeth, N.J., to Chicago.
The train struck the rear of the parked freight train around 11:32 a.m. at 48th Street and Shields Avenue, Rodriguez told WBBM.
Norfolk Southern spokesman Rudy Husband said he had no details about what caused the accident or what the freight train was carrying.
Amtrak spokesman Derrick James said it was unclear which train was in the wrong place. He said Amtrak shares the track with Norfolk Southern, which owns it. He also said he did not know if the freight train was moving or stationary when it was struck.
James said Amtrak was awaiting information from an event recorder, a device similar to the black boxes on airliners. The National Transportation Safety Board sent investigators.
James said of particular interest is what the signals were before the Amtrak train got to the spot where the collision occurred.
Interim Police Superintendent Dana Starks said the accident was recorded by a camera on a nearby post and the footage would be turned over to investigators.