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The 28-year-old -- who appears to have gained United manager Jose Mourinho's trust after failing to do so when they were both at Chelsea -- will be out for an unspecified amount of time, the club said in a statement.
"Juan has had surgery for a groin injury. Further updates on his recovery will follow in due course," read the statement.
Mata's news follows that of "long term" injuries as Mourinho termed it to both England international defenders Chris Smalling (calf) and Phil Jones (toe).
Mourinho will also have to do without the suspended Ander Herrera and Zlatan Ibrahimovic for Saturday's Premier League match at home to West Brom as well as the world's most expensive player Paul Pogba who has a hamstring problem.
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United face a daunting run with nine games in April.
They are battling on two fronts to try and secure Champions League football next season, to finish in the top four in the Premier League or if that fails by winning win the Europa League -- they face Belgian side Anderlecht in the quarter-finals.