Metra said that six Union Pacific West Line trains - four inbound and two outbound - were canceled. A few trains were also delayed.
The first train affected was scheduled to leave Elburn at 4:48 a.m. The line offer service from the western suburbs to the Ogilvie Transportation Center in downtown Chicago. By 4 p.m., trains were moving according to schedule.
Union Pacific, which is responsible for the engineers, said the crew shortages were caused by a combination of vacations, family leave and illness.
"We apologize for this inconvenience and we'll be working very hard to get to the bottom of it and make sure it doesn't happen again," said Mark Davis, spokesman, Union Pacific.
But some commuters question whether scheduling issues were the real cause of the delays and cancellations.
"The fact that they are saying a combination of vacation and sick days, I don't see that being any perfect storm you couldn't prepare for," said Axel Cerny.
"I think it is a work stoppage. It never happened before. It's highly unusual," said Steve Damman.
Union Pacific, Metra and the union representing the engineers all say the problems had nothing to do with a job action.
The Brotherhood of Locomotive Engineers and Trainmen president Dennis Pierce says in a written statement, "this morning's disruptions were in no way caused by the locomotive engineers represented by BLET. There is an ongoing general crew shortage on the up because of Midwest flooding."
The cancellations left many passengers stranded.
"My wife and I have been debating on whether we are going to drive in or just wait it out," commuter Steve Dammann told ABC7.
"If I have to, I'll try to take a bus up on Lake Street and get to the 'L' stop in Oak Park and get on there, but it would be very, very inconvenient," said Carolyn Winter.
Many delayed commuters were relieved to finally make it downtown.
"It still beats driving," one commuter said.
On their website, Metra called the entire situation unacceptable.
- Canceled trains:
- Outbound Train #17, 6:57 a.m.
- Inbound Train #24
- Inbound Train #28
- Inbound Train #16, 6:03 a.m.
- Outbound train #13, 5:53 a.m.
- Inbound Train #10, 4:48 a.m.
Outbound train #15, scheduled to arrive at Elburn at 7:50 a.m., made 10 to 15 minute delays and extra stops.
Get the latest from Metra at metrarail.com