Kennedy, one of the most contentious appointees Trump has announced for his cabinet, needs Senate confirmation to take up the position in January and faces an uphill climb due to his longstanding reputation as a conspiracy theorist who promotes health misinformation.
Trump was asked by reporters at his beachside club in Florida to respond to criticism that Kennedy's enmity for inoculations could lead to children being harmed. He called his nominee a "highly respected man who has run an incredible company."
"I think he's going to be much less radical than you would think," Trump said. "I think he's got a very open mind, or I wouldn't have put him there."
Trump added that he himself had been against mandating the Covid-19 shot in schools during the 2020 pandemic and appeared open to the possibility that vaccines cause autism -- a widely debunked claim that stems from a retracted British study from the 1990s.
"We're going to look into finding why is the autism rate so much higher than it was 20, 25, 30 years ago?" he said.
"I mean, it's like, it's 100 times higher. There's something wrong, and we're going to try finding that."
While autism is indeed diagnosed much more frequently now than in the past, research suggests that the increase is due to changes to diagnostic criteria, increased awareness and better screening.
Multiple studies have uncovered no evidence of a connection between vaccination and autism.
Trump's own record on vaccines is spotty.
During his first term, he oversaw Operation Warp Speed, calling the landmark mission to create a Covid-19 shot in record time "one of the greatest miracles of the ages."
And on Monday he told reporters he was a "big believer" in the polio vaccine.
But Trump began publicly musing about a link between vaccines and autism a decade before his first term in office.
He was asked Monday if schools should force children to get shots and he responded that he was "not a big mandate person" and suggested he had been against vaccine requirements during the pandemic.
During a wide-ranging press conference, Trump also vowed to work with Kennedy -- known as RFK Jr -- to reduce America's sky-high prescription drug costs by eliminating "middlemen" who had got "rich as hell."
Trump ordered a $35-per-month cap on insulin in his first term for some welfare recipients but it was President Joe Biden that made the restriction permanent and vastly expanded its beneficiaries by signing a law.
Kennedy, who has said he does not plan to take vaccines off the market, is set to meet with at least 25 Republican senators this week and can afford to lose only three in total in his confirmation hearing early next year if Democrats all vote against him.
