Joint Chiefs of Staff chairman General Mark Milley said on Monday that the men were "in a secure facility".
Gen Milley also announced that Baghdadi's remains had been disposed of and there were currently no plans to share footage of his death.
Baghdadi killed himself during the Saturday raid in Syria, the US says.
"Baghdadi's remains were transported to a secure facility to confirm his identity with forensic DNA testing and the disposal of his remains has been done and is complete and was handled appropriately," Gen Milley told reporters at the Pentagon.
Gen Milley - who is the highest-ranking member of the US military - said photos and video were going through "a declassification process".
There were no further details about the detained men.
Baghdadi died from detonating a suicide vest after fleeing into a tunnel, chased by US military dogs, President Donald Trump announced during a news conference on Sunday.
Mr. Trump had earlier suggested he might release some footage of the raid.
In response to a question about Mr. Trump's contention that Baghdadi had whimpered and cried before his death, Gen Milley said he was not aware where the information came from but added: "I assume it was [from] talking directly to unit members."
Gen Milley also said that US troops would continue to protect oilfields from IS militants, though "at the end of the day, we will be sending troops home".
"But in the meantime, we're going to make some other moves to ensure that we can accomplish that mission of securing the oilfields in order to deny them access to Isis [IS]."
Mr. Trump has said the US should be able to take some of the oil, but critics say doing so would violate the Geneva Convention's laws against pillaging natural resources.
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