Approximately 2,300 of those canceled flights are from Chicago-based United Continental, and 1,300 were Delta flights. U.S. Airways canceled more than 1,100 flights.
The five main New York-area airports closed Saturday afternoon.
Operations at Chicago's O'Hare were normal early Saturday, except for travel to and from the East Coast. As of late Saturday, 200 flights had been cancelled. At Midway Airport, 30 flights had been cancelled. Airline officials say many cancelations will be in effect throughout the weekend.
ABC7 spoke to some passengers arriving on some of the last flights to Chicago from East Coast cities Saturday morning.
"We really thought we weren't going to make the flight because we had to check in, security was crowded. It was packed, but we made it," Thea Wells said.
Many passengers at O'Hare were trying to escape the storm Friday night or were trying to get back to their homes on the East Coast before the hurricane hit. Among them, Heather Silveira, who suspended her job search in New York. She said she would wait out the storm in Chicago with her aunt.
"It's frustrating, so hard leaving because it's like you don't know if it's going to be bad or if I'm just leaving for nothing. But it's better to be safe than be caught in a storm," she said.
As for other forms of travel, Amtrak has cancelled much of its service from Chicago eastward.
At the Greyhound station in the West Loop, there's a bus available for those who are stranded, which is a bit more comfortable than sitting in the terminal.
For the past three nights, it's been home for Jim Nicholson, who's trying to get to Baltimore from Minneapolis.
"You can't predict it with the storm -- just how bad the damage is, how long the cleanup is going to take and so forth. Even if the storm passes through, it could be quite awhile with power lines down and so forth," Nicholson said.