People took to Twitter to air their grievances at the airline as queues piled up at Terminal 5 while the check-in system issue was dealt with.
It seems BA are getting used to fixing the problem as this time the system was back and running after a short period.
One Twitter user was concerned about missing her flight as a result of the issue.
Another @phcd30 tweeted about being stranded at Heathrow.
And the nightmare continued.
It seems domestic flights including to Manchester and Newcastle have been hit by flight cancellations, much to the dismay of travellers.
It is unclear whether this is to do with the with the IT problem which BA said when we contacted them at 5.30pm had been fixed.
A British Airways spokesperson said: “Our IT teams worked very hard to quickly fix a short-lived problem with our check-in system.
“We are sorry for the delays some customers had as they checked-in for their flights.”
BA has said everything is back up and running.
In addition, passengers may like to know the Heathrow Connect service is operating a reduced half hourly service between London Paddington and Heathrow due to engineering works.
The new check-in system failed weeks earlier on July 7 and before that in June.