The outage affected airports including JFK, San Francisco and Denver, as global travelers arrived from holiday travels on New Year's Day.
As Reuters notes, a similar outage occurred at the same time previous year, so it might be that the customs systems were slammed with Christmas travelers and couldn't handle the excess traffic.
Computer issues at U.S. Customs and Border protection at JFK Airport caused lines and major headaches for travelers at JFK Airport.
The agency said it had access to the national security-related databases during the outage.
Contact your airline provider and airport to determine if your flight has been affected.
One person tweeted that Miami Airport is "total chaos" while another said the lengthy lines at JFK "are horrible". No indication the disruption was malicious in nature.
CBP said it "took immediate action to address the technology disruption".
During the outage, "alternative procedures" were used to process worldwide passengers, according to the agency.
CBP has not given any further explanation of what caused the disruption in the system.
CBP said travelers at "some ports of entry experienced longer than usual wait times".