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Stanton, 24, will be out for the hectic Christmas period after tearing the lateral meniscus in his right knee.
He will undergo surgery on Thursday. Stanton suffered a similar injury at the start of 2005 during the New Years Day game with Darlington.
Manager Brian Laws told the Scunthorpe Telegraph: "It's a hammer blow for us, there's no doubt about that.
"Things are not going to plan for us at the moment, but we have some big games coming up and we have to keep focused if we want to be where we want to be."