The 40-year-old has been suffering severe back pain and was taken to hospital after last night's 1-0 league victory at Valencia that left the Catalans 10 points at the top of the table.
Despite deciding to attend the match with acute discomfort in his lower back, there are now doubts over whether he will be able to make it to the touchline for the second leg with the Gunners.
Guardiola’s No 2 Tito Vilanova said: ‘Pep is not feeling great and he got through the match as best he could. He is having a bad time of it and he doesn’t even know where to put himself.’
Guardiola had to cancel a press conference on Tuesday because of his back problems.
Barcelona face struggling Real Zaragoza at home on Saturday before meeting Arsenal three days later looking to overturn a 2-1 first leg defeat and knock the Londoners out of the tournament for the second successive year.
Also from Twitter: Barca have confirmed Pep Guardiola has a herniated disc, no word yet on whether he'll have an operation.
Get better soon Pep