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Kompany had been unwell with a virus and missed the pre-match press conference against Arsenal in the Champions League in midweek, although he was on the touchline during the match.
An official statement read: “Vincent Kompany required medical attention after collapsing during an FC Bayern reserve team training session on Friday.
“The first-team head coach was watching the second string’s session. Kompany is undergoing thorough examinations in hospital and will remain under medical care. His coaching staff will oversee training and match activities until further notice.”
Director of sport Max Eberl added: “Vincent Kompany’s health is our top priority. We at FC Bayern will do everything we can to ensure he makes a speedy recovery.
“Vinnie is receiving all the necessary medical care and support, and all the time he needs. His coaching team, in whom we have complete confidence, will take over his duties. All of us at FC Bayern wish Vinnie a speedy recovery.”
Kompany spent two seasons in charge at Turf Moor, initially leading the Clarets to the Championship title and passing the 100-point milestone. His side was relegated from the Premier League the following campaign.
The 40-year-old left Burnley in the summer of 2024 to take charge of the German giants and has won back-to-back Bundesliga titles.