The classy centre-back was a contender for a place in Fabio Capello's World Cup squad but the news will be most sorely felt in the short-term at The Reebok Stadium.
Cahill, 24, is a key figure for Owen Coyle's side but the Trotters manager has tried to focus on the positives after the reason for the stopper sitting out the drab 0-0 draw with Fulham was revealed.
Coyle said: "Gary suffered a pain in his arm and it became severely swollen on the day of the game.
"There was no way he could play so we took him straight off to hospital.
"It turns out he had a blood clot in his arm, so he is going to be out for a number of months.
"It is a severe blow for the boy but our main concern is his welfare. We have to make sure Gary is fit and well.
"He will miss the next few months, it might be for the rest of the season, we will hear from the specialist later.
"The clot needed to be resolved and, in doing that, you need the medication. It follows you can't play.
"As disappointed as we are, at 24, Gary has a marvellous career ahead of him.
"I believe he would have made the World Cup for the summer but we have to make sure, first of all, he recovers from this blood clot.
"He is a terrific lad and someone we love working with. He has a great mindset.
"Gary will get the best care available to him. As much as we love football, we will focus on making sure Gary recovers well."
Coyle added that he believes the injury is not sport-related.
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