The 58-year-old suggested his team were not awarded a penalty by referee Phil Dowd in their FA Cup third-round replay because they were the away side at Old Trafford
Following West Ham's 1-0 loss at Old Trafford on on January 16, Allardyce had claimed that referee Phil Dowd judged penalty decisions for either team differently because "Jordan [Spence] plays for West Ham away against Manchester United and Rafael plays at home at Old Trafford".
Allardyce has now requested a personal hearing with the FA.
A statement from the FA reads: "West Ham United manager Sam Allardyce has denied an FA charge of misconduct in relation to media comments.
"The comments followed his side’s FA Cup with Budweiser Third Round replay against Manchester United at Old Trafford on 16 January 2013.
"It is alleged Allardyce questioned the integrity of the match referee and/or match officials in general, and/or implied that the match referee and/or match officials in general were motivated by bias; and/or brought the game into disrepute in contravention of Rule E3(1).
"Allardyce has requested a personal hearing, the date of which will be set in due course."