But since his return from injury Holden has been widely regarded as one of Bolton's best players and has helped them to seventh place in the Premier League.
"First and foremost, our main concern is Stuart and his recovery," said Bolton manager Owen Coyle.
"He will get all the time and support he needs. Stuart has been outstanding this season and has shown he is one of the best midfielders in the Premier League.
"He has such desire, strength of character and a winning mentality and he will draw on those attributes in his rehabilitation."
Former Bolton player Alan Gowling told BBC Radio Manchester that Holden's injury was a huge blow to both player and club.
"He's a key man in that midfield and, for me, when he was injured earlier in the season, Bolton went off the boil a little bit," said Gowling.
"It was when Stuart returned that Bolton's game seemed to pick up, so I think he'll be a big miss.
"For me he's the jewel in Bolton's crown, he's an excellent player, he's got a great future and obviously it will be a blow in the short term, and they will be looking for someone like Mark Davies to take on the role."
Holden joined Bolton in January 2010 from Major League Soccer club Houston Dynamo and signed a contract extension in September that is set to keep him at the Trotters until 2013.
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