The former Tranmere ace had just returned to action in recent weeks following an ankle problem, but he suffered a recurrence against Sheffield United and is expected to be missing for a substantial period.
Stoke boss Tony Pulis admitted it was a major blow to lose the central defender to injury.
"Losing Clint is a real blow," Pulis told the club's official website.
"It's a problem with his ankle again and he looks like he could be out for a while.
"I thought while he was on the pitch that was the best our back four had looked in a long time. We looked very strong and Sheffield were not causing us any problems."
