The MSF facility is seen as a key medical lifeline in the region and has been running 'beyond capacity' during recent fighting that saw the Taliban seize control of the provincial capital for several days.
The strike early today left the building engulfed in flames, with photos posted by MSF on Twitter showing shocked and dazed staff in the aftermath of the bombing.
"At 2:10 am (2040 GMT) local time... the MSF trauma centre in Kunduz was hit several times during sustained bombing and was very badly damaged," it said in a statement.
"Three MSF staff are confirmed dead and more than 30 are unaccounted for. The medical team is working around the clock to do everything possible for the safety of patients and hospital staff."
NATO said US forces may have been behind the strike.
"US forces conducted an air strike in Kunduz city at 2:15 am (local time)... against individuals threatening the force. The strike may have resulted in collateral damage to a nearby medical facility. This incident is under investigation”, a NATO statement said.


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