Rooney will miss United's trip to Newcastle on Saturday after manager David Moyes revealed the striker was struggling with a 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 is injured. He has a badly bruised toe so he won't be involved against Newcastle. It will be touch and go for Wayne for Wednesday," Moyes told reporters on Friday.
"It's a toe injury and they're never easy when you get one. You could see him limping in the game - towards the end, quite badly.
"He has a bad toe. There's not an awful lot you can do with a toe injury. Sometimes you can feel better quite quickly with them and sometimes you need an injection to play with it if it's bruising.
"With a lot of toe injuries, you have to make sure there isn't a hairline fracture or crack in your toe. We will have all that checked."
England manager Roy Hodgson will be sweating on the news, with there being a possibility of a hairline fracture, which could mean several weeks on the sidelines.
That would severely hamper Hodgson's plans ahead of the FIFA World Cup in Brazil, which is just over two months away.
Foot injuries have plagued Rooney throughout his career and played a significant part in his inability to perform for England in football's showcase event.
Just six weeks out from England's 2006 World Cup Group B opener against Paraguay, Rooney fractured his metatarsal bone after an innocuous challenge by Chelsea's Paulo Ferreira in United's 3-0 defeat at Stamford Bridge.
Rooney was expected to be sidelined for the group stages but featured in all but one game as England were eliminated by Portugal in the quarter-finals.
He went goalless throughout the tournament.
Fast forward four years and Rooney also went into the 2010 World Cup under an injury cloud after damaging his ankle during United's 2-1 loss to Bayern in Munich.
Rooney started all three Group C matches but failed to find the back of the net in another disappointing campaign for England.
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