As of 9 a.m. Saturday, more than 600 flights were cancelled at O'Hare; more than 24 have been reported cancelled at Midway. However, some flights are also leaving on-time as scheduled. As many as 1,500 flights were cancelled at O'Hare Friday.
Southwest Airlines said flights will continue to operate at a reduced rate Saturday.
"Yesterday we were very optimistic that we would be able to operate close to a full schedule today, coming in this morning, doesn't look like that's going to happen, sounds like the airspace restrictions will continue throughout the day, so we're going to work hard to be able to serve as much we can," a Southwest Airlines spokesperson said.
Southwest cancelled all flights out of Midway Airport late Friday afternoon, affecting 450 flights, which also affected travel at Milwaukee's Mitchell Airport.
Joe Harrison, a traveler, stayed at a hotel near O'Hare overnight, but got a flight out of Chicago Saturday morning.
"Just the fear of not knowing, but again, once we found out what exactly was going on, we understood it, and we were able to make nice, sound and informed decisions," he said.
The ground stop was triggered by a fire at an FAA facility in Aurora. It was lifted at 11 a.m., but planes are moving at a "reduced rate." The headaches could continue for travelers for days due to extensive damage at the FAA facility.
PHOTOS: Fire at regional FAA facility grounds Chicago flights
Airlines are urging travelers to check the status of their flights at www.fly.faa.gov.
Officials said the fire at the FAA facility was intentionally set, but is not considered a terrorist attack.
VIDEO: Fire set at FAA facility, police say