Rooney limped away from Old Trafford after scoring his 32nd goal of the season in the 2-1 win over Liverpool on Sunday after suffering a recurrence of the injury.
Injury doubt: Rooney battles with Jamie Carragher during Manchester United's clash with Liverpool on Sunday
The injury could become a major worry for United as they chase glory at home and abroad, and England manager Fabio Capello will also be monitoring the situation with the World Cup fast approaching.
The problem arose ahead of last month's Carling Cup final, when he came off the bench to replace the injured Michael Owen.
Four days later he played at Wembley again, for England against Egypt, much to the displeasure of United boss Sir Alex Ferguson.
On the spot: Wayne Rooney scored United's equaliser on Sunday
Meanwhile the FA are examining footage of Fernando Torres scuffing the penalty spot ahead of Rooney's equaliser against Liverpool.
United are two points clear of Arsenal in this fascinating title race, but face a difficult run-in.
After the Bolton clash, they face a showdown with fellow title rivals Chelsea on Easter Saturday, which falls between their two European Cup matches against Bayern Munich.
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