Delays were mainly seen on the eastern half of the country.
The delays, according to the Federal Aviation Administration appeared minor. But passengers told a different story. They talked about delays of two hours or more. And on a clear day in Chicago, it had nothing to do with the weather.
The problem was an FAA computer in Hampton, Ga., near Atlanta, not allowing pilots to file flight plans and affecting major airports, which began about 1:30 Tuesday afternoon. Flight plans had to be inputted manually after a computer glitch, which takes more time. The FAA said they worked to fix the problem as quickly as they could, but stuck passengers were getting impatient.
"I stopped over for a 45-minute delay and we have been here for the last two hours," said air traveler Robin Crocker.
The problem is fairly similar to another hiccup in Chicago that caused major delays in June. A similar problem last week caused 100 delays.
The FAA said the glitch caused no safety issues. The tower and air traffic controllers were still able to communicate with the pilots, so there were no problems once passengers were in the air.
Passengers heading to Midway Tuesday afternoon knew there could be problems, but most said they were pleasantly surprised.
"They made it sound like all of the flights in the country were delayed, but it isn't that bad. We were worried at first, but doesn't sound as bad as we thought," said Mattias Keese.
"I was a little concerned. My husband was going to Denver, and they were saying we might be delayed. And I said, 'I see on the board, seems like it's on time,'" said Patricia Collins.
At the height of the problem, some passengers had been on the plane for two hours on the tarmac, and then they were told that the plane couldn't take off, so they had to return to the terminal.
"As you can see, there are no lines, no heavy traffic around here, but when things happen within the airline system, sometimes things that happen on the East Coast will have a domino effect," said Karen Pride, Department of Aviation.
The cause of the glitch is unknown, but terrorism has been ruled out.
Not all airports in the U.S. were affected. You can see real time which airports are being affected at www.fly.faa.gov.
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The Associated Press contributed to this report.