(CNN) -- American Airlines grounded flights nationwide on Tuesday due to problems over several hours with its computerized reservation system.
The decision also resulted its regional affiliate, American Eagle, holding flights at Dallas Ft. Worth, Chicago's O'Hare and New York LaGuardia -- all major airports for the carrier's domestic operations.
The glitch caused big delays and flight cancellations for the company, which sought court approval on Monday to exit bankruptcy. It plans to merge with US Airways.
American CEO Tom Horton apologized the customers in a video Tuesday evening, saying that the glitch was "a software issue impacting both primary and backup systems."
Bad weather often forces airlines to halt flights in specific regions, but a nationwide grounding is highly unusual.
American estimates it flies about 275,000 passengers a day and receives more than 239,000 reservations calls.
American first reported computer problems via twitter at noon ET, then announced a ground stop one hour later.
Its reservation systems were restored by 4:30 p.m., but the company said passengers could expect delays and cancellations throughout the day.
The Federal Aviation Administration also confirmed that American had sought permission to hold flights.
The carrier said in a statement that it saw "no evidence" that the technical outage was in any way related to Monday's deadly bombing in Boston that is under investigation as an act of terrorism.
Airlines have long been a target of overseas terrorists, although U.S. officials say they have not determined whether the origin of the Boston attack was domestic or foreign.
American's reservation systems are operated by the technology company Sabre, which told CNN that its systems were functioning, but American had trouble connecting.
DFW, where American operates 85% of daily flights, used buses to help get passengers off planes because gates were full of aircraft that had not departed, spokesman David Magaña said.
Inside the terminal there were some longer lines and the airport was more crowded than it would be on a day with normal operations.
The carrier apologized to passengers and said they could rebook on another airline if they must travel on Tuesday and were already at the airport.
American was also willing to honor fare differences for rebooked travel, in certain cases, or offer refunds in other circumstances.
CNN's Devon Sayers and Mike Ahlers contributed to this report.