The England striker has sustained a toe injury and faces a race against time to get fit in time for the Champions League quarterfinal second leg tie in Germany.
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Rooney will miss United's trip to Newcastle on Saturday after manager David Moyes revealed the striker was struggling with the toe injury he sustained during last Tuesday's 1-1 draw against Bayern at Old Trafford.
The 28-year-old, who injured his ankle at the Allianz Arena in 2010, is now a doubt for the trip to Munich for the club's do-or-die clash with Bayern on Wednesday.
"Wayne's got a badly bruised toe," Moyes told MUTV. "He picked it up in the game the other night. Whether we were going to play him or rest him, it doesn't matter.
"He's got a terrible toe and not only will it be a problem for this game, it could be a problem for the Munich game as well on Wednesday.
"So we need to monitor it. We'll get him treatment all over the weekend and see if we can speed it up."
England manager Roy Hodgson will also be monitoring developments closely, as an injury to his star man would seriously hamper his preparations for the World Cup.