Many of President-elect Donald Trump’s candidates for federal health agencies have promoted policies and goals that put them at odds with one another or with Trump’s choice to run the Department of Health and Human Services, Robert F. Kennedy Jr., setting the stage for internal friction over public health initiatives.

The picks hold different views on matters such as limits on abortion, the safety of childhood vaccines, the COVID-19 response and the use of weight-loss medications. The divide pits Trump picks who adhere to more traditional and orthodox science, such as the long-held, scientifically supported findings that vaccines are safe, against often unsubstantiated views advanced by Kennedy and other selections who have claimed vaccines are linked with autism.

A situation in which high-ranking policy makers are on the same team with such varying views could make it harder to develop and pursue priorities. 

The Trump transition team and the designated nominees mentioned in this article did not respond to requests for comment.

It’s a potential “team of opponents” at the government’s health agencies, said Michael Cannon, director of health policy studies at the Cato Institute, a libertarian policy organization. Kennedy doesn’t have a medical degree. 

Kennedy, he said, is known for rejecting opposing views when confronted with science.

“The heads of the FDA and NIH will be spending all their time explaining to their boss what a confidence interval is,” Cannon said, referring to a statistical term used in medical studies.

Those whose views prevail will have significant power in shaping policy, from who is appointed to sit on federal vaccine advisory committees to federal authorization for COVID vaccines to restrictions on abortion medications. If confirmed as HHS secretary, Kennedy is expected to set much of the agenda.

“If President Trump’s nomination of RFK Jr. to be secretary is confirmed, if you don’t subscribe to his views, it will be very hard to rise in that department,” said Amesh Adalja, an infectious disease specialist and senior scholar at the Johns Hopkins Center for Health Security. “They will need to suppress their views to fit with RFK Jr’s. In this administration, and any administration, independent public disagreement isn’t welcome.”

Kennedy is chair of Children’s Health Defense, an anti-vaccine nonprofit. He has vowed to curb the country’s appetite for ultra-processed food and its incidence of chronic disease. He helped select Trump’s choices to lead the Centers for Disease Control and Prevention, the Food and Drug Administration and the National Institutes of Health. If confirmed, he would lead them from the helm of HHS, with its more than $1.7 trillion budget.

Clashes are likely. Kennedy has supported access to abortion until a fetus is viable. That puts him at odds with Dave Weldon, the former Florida congressman whom Trump has chosen to run the CDC. Weldon, a physician, is an abortion opponent who wrote one of the major laws allowing health professionals to opt out of participating in the procedure.

Weldon would head an agency that’s been in the crosshairs of conservatives since the COVID pandemic began. He has touted his “100% pro-life voting record” on his campaign website. (He unsuccessfully ran earlier this year for a seat in Florida’s House of Representatives.)

Trump has said he would leave decisions about abortion to the states, but the CDC under Weldon could, for example, fund studies on abortion risks. The agency could require states to provide information about abortions performed within their borders to the federal government or risk the loss of federal funds.

Weldon, like Kennedy, has questioned the safety of vaccines and has said he believes they can cause autism. That’s at odds with the views of Marty Makary, a Johns Hopkins surgeon whom Trump plans to nominate for FDA commissioner. The British American said on the “Brian Kilmeade Show” on Fox News Radio that vaccines “save lives,” although he added that it’s good to question the U.S. vaccine schedule for children.

The American Academy of Pediatricians encourages parents and their children’s doctors to stick to the recommended schedule of childhood vaccines. “Nonstandard schedules that spread out vaccines or start when a child is older put entire communities at risk of serious illnesses, including infants and young children,” the group says in guidance for its members.

Jay Bhattacharya, a doctor and economist who is Trump’s selection to lead NIH, has also supported vaccines.

Kennedy has said on NPR that federal authorities under his leadership wouldn’t “take vaccines away from anybody.” But the FDA oversees approval of vaccines, and, under his leadership, the agency could put vaccine skeptics on advisory panels or could make changes to a program that largely protects vaccine makers from consumer injury lawsuits.

“I do believe that autism does come from vaccines,” Kennedy said in 2023 on Fox News. Many scientific studies have discredited the claim that vaccines cause autism.

Ashish Jha, a doctor who served as the White House COVID response coordinator from 2022 to 2023, noted that Bhattacharya and Makary have had long and distinguished careers in medicine and research and would bring decades of experience to these top jobs. But, he said, it “is going to be a lot more difficult than they think” to stand up for their views in the new administration.

It’s hard “to do things that displease your boss, and if [Kennedy] gets confirmed, he will be their boss,” Jha said. “They have their work cut out for them if they’re going to stand up for their opinions on science. If they don’t, it will just demoralize the staff.”

Most of Trump’s picks share the view that federal health agencies bungled the pandemic response, a stance that resonated with many of the president-elect’s voters and supporters — even though Trump led that response until Joe Biden took office in 2021.

Kennedy said in a 2021 Louisiana House oversight meeting that the COVID vaccine was the “deadliest” ever made. He has cited no evidence to back the claim.

Federal health officials say the vaccines have saved millions of lives around the globe and offer important protection against COVID. Protection lasts even though their effectiveness wanes over time.

The vaccines’ effectiveness against infection stood at 52% after four weeks, according to a May study in The New England Journal of Medicine, and their effectiveness against hospitalization was about 67% after four weeks. The vaccines were produced through Operation Warp Speed, a public-private partnership Trump launched in his first term to fast-track the shots as well as other treatments.

Makary criticized COVID vaccine guidance that called for giving young children the shots. He argued that, for many people, natural immunity from infections could substitute for the vaccine. Bhattacharya opposed measures used to curb the spread of COVID in 2020 and advised that everyone except the most vulnerable go about their lives as usual. The World Health Organization warned that such an approach would overwhelm hospitals.

Mehmet Oz, Trump’s choice to head the Centers for Medicare & Medicaid Services, an agency within HHS, has said the vaccines were oversold. He promoted the use of the anti-malaria drug hydroxychloroquine as a treatment. The FDA in 2020 revoked emergency authorization of hydroxychloroquine for COVID, saying that it was unlikely to be effective against the virus and that the risk of dangerous side effects was too high.

Janette Nesheiwat, meanwhile, a former Fox News contributor and Trump’s pick for surgeon general, has taken a different stance. The doctor described COVID vaccines as a gift from God in a Fox News opinion piece.

Kennedy’s qualms about vaccines are likely to be a central issue early in the administration. He has said he wants federal health agencies to shift their focus from preparing for and combating infectious disease to addressing chronic disease.

The shifting focus and questioning of vaccines concern some public health leaders amid the spread of the H5N1 bird flu virus among dairy cattle. There have been almost 60 human infections reported in the U.S. this year, all but two of them linked to exposure to cattle or poultry.

“Early on, they’re going to have to have a discussion about vaccinating people and animals” against bird flu, said Georges C. Benjamin, executive director of the American Public Health Association. “We all bring opinions to the table. A department’s cohesive policy is driven by the secretary.”

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