Thomas Machowicz | Reuters

President-elect Donald Trump has tapped Robert F. Kennedy Jr. to lead the Department of Health and Human Services – a selection that is raising fears in the public health community and leaving the biotech and pharmaceutical industries bracing for disruptions to drug development.

Trump's announcement on Thursday gives Kennedy, a notorious vaccine skeptic, a good chance of securing the nation's top health-care job. The coming Republican-held Senate will ultimately decide whether to confirm him, though Trump has raised the prospect of sidestepping that process with recess appointments.

If confirmed, Kennedy will take the reins of a $1.7 trillion agency that oversees vaccines and other medicines, scientific research, public health infrastructure, pandemic preparedness, food and tobacco products. HHS also manages government-funded health care for millions of Americans – including seniors, disabled people and lower-income patients who rely on Medicare, Medicaid, and the Affordable Care Act's markets.

The heads of the Food and Drug Administration, Centers for Disease Control and Prevention, National Institutes of Health and Centers for Medicare & Medicaid Services all report to the HHS secretary, though Trump has yet to nominate them. Kennedy will likely have some influence over who the president-elect chooses for those roles, health policy experts said.

Some health policy experts told CNBC that Kennedy could elevate vaccine skepticism and deter more Americans from taking recommended shots, attempt to cut funding or entire departments at different agencies, and shift research and development toward more alternative treatments or disease areas of interest to him, among other efforts.

Kennedy's so-called Make America Healthy Again platform argues a corrupt alliance of drug and food companies and the federal health agencies that regulate them are making Americans less healthy. Kennedy has long contended that the agencies that HHS oversees need reform or a sweeping overhaul, part which could mean cutting funding, purging staff and hiring new employees who share his often disproven views on health and science.

He has also said he wants to remove fluoride from drinking water systems and target chronic diseases by cracking down on food and chemical additives, among other efforts.

But there will be some limits to Kennedy's power – even with a Republican government trifecta. Some of his proposals, such as cutting funding, may not easily pass through Congress. Other efforts could spark expensive and prolonged litigation against the federal government.

Spokespeople for Kennedy and Trump's campaign did not immediately respond to requests for comment.

Here are some of the things that Kennedy may – or may not – be able to accomplish as HHS secretary.

Vaccines

Christina House | Los Angeles Times | Getty Images

Kennedy is a staunch critic of vaccines, which have saved the lives of more than 1.1 million children in the U.S. and saved Americans $540 billion in direct health-care costs over the last three decades, according to CDC research released in August.

He has long made misleading and false statements about the safety of shots. He has claimed they are linked to autism despite decades of studies that debunk that association. Kennedy is also the founder of the nonprofit Children's Health Defense, the most well-funded anti-vaccine organization in the U.S.

Ultimately, Kennedy's influence over immunization policy could lead to an increase in diseases preventable by vaccines, several health policy experts told CNBC.

"He could create considerable distrust in vaccines and make some vaccines highly politicized, so in particularly red states, we could see outbreaks of fully preventable childhood diseases," said Lawrence Gostin, a health law and policy expert at Georgetown University. That includes measles, mumps, rubella and polio.

Despite his history, Kennedy told NBC News in early November that he isn't planning to take anyone's vaccines away in the U.S.

That would be a difficult task, experts said. The FDA can pull a product from the market if further trials after approval fail to confirm that its clinical benefits outweigh its risks, or if unexpected risks are detected among patients. That has not been the case with the approved shots on the market.

"It would be hard to imagine that a new HHS secretary would be able to immediately remove vaccines that are already approved and already being used and recommended by the government from the market," said Josh Michaud, associate director of global health policy at KFF, a health policy research organization. "He can't just make that change with a simple wave of a wand."

Still, Kennedy has repeatedly argued that there is not enough data on vaccines and their effects. He told NPR earlier this month that the Trump administration is going to "make sure those scientific studies are done and that people can make informed choices about their vaccinations and their children's vaccinations."

As HHS secretary, Kennedy could "cherry-pick" data from additional government studies and release misleading results that undermine trust in the safety and efficacy of vaccines, Gostin said.

That misinformation could deter some Americans from receiving certain shots. Michaud added vaccine misinformation could push health officials on the state and local level to "perhaps allow for more individual choice rather than mandating routine vaccination" for certain diseases.

Many state health departments and clinicians rely on vaccine recommendations from an advisory committee to the CDC. Those include who should get what shots and at what age.

Those guidelines have broader implications for public health. Vaccines recommended by that advisory panel and approved by the CDC director are covered under the Affordable Care Act. The agency also administers the Vaccines for Children program, which provides free vaccines for children in low-income families.

Kennedy could attempt to influence that CDC advisory committee and a similar panel linked to the FDA by stacking them with people who hold anti-vaccine views, Gostin said. The HHS secretary has the power to form an advisory committee, remove members, and set the terms and qualifications for them.

That could produce more limited vaccine recommendations that aren't firmly rooted in science, he added. It could also translate to a "fragmentation of vaccine policy" across the U.S. if only some states accept recommendations from advisors selected by Kennedy.

Federal agency funding, staffing

Kennedy in recent weeks has pledged to end what he calls "corporate corruption" at federal health agencies and purge staff when he steps into his role in the Trump administration.

He has said he would clear out "entire departments" at the FDA, saying that workers who stand in the way of approval of several controversial or dubious treatments should prepare to "pack their bags."

Kennedy, before dropping out of the presidential race, also said he wanted to shift NIH's focus away from infectious disease and toward chronic diseases like obesity for eight years. In September, Kennedy said half of the NIH's $48 billion budget should go toward "preventive, alternative and holistic approaches to health."

A shake-up at the NIH – the largest public funder of biomedical research in the U.S. – could have major implications for research and the pharmaceutical industry. The NIH funds and conducts research on everything from vaccines and cancer to new drug targets, laying the groundwork for treatments that companies can develop.

"He could certainly allocate funding away from drugs that he's not interested in and more towards maybe areas that are more speculative," said Genevieve Kanter, associate professor of public policy at the University of Southern California.

Kanter pointed to his long history of embracing disproven treatments, such as claiming that hydroxychloroquine and ivermectin work against Covid, even though several studies say they do not. Hydroxychloroquine is an immunosuppressive drug, while ivermectin is used to treat infections caused by parasites.

Major changes or funding cuts at the NIH, FDA and CDC would require congressional approval. Federal employees are also protected against arbitrary or politically motivated firing.

FDA staff are further shielded because Congress does not fully fund their salaries. Nearly half of the agency's $7.2 billion budget this year came from so-called user fees, or payments made by drug and medical device manufacturers to fund the staff resources needed to quickly review their products, conduct inspections and ensure the safety of clinical studies.

It seems "unlikely" that Kennedy would be able to end that user fee program, according to Richard Frank, director of the Center on Health Policy at Brookings. But he may attempt to influence negotiations around how the program is implemented when Congress decides whether to reauthorize it after 2027, Frank said.

Gostin said other "cuts across the board" at the three agencies are possible, especially in areas that are "part of the culture wars." The CDC could see funding reduced for key functions related to vaccines, chronic disease, sexual and reproductive health, and firearm injury and prevention, according to Gostin.

He added that the FDA's nutrition departments could also see cuts or be "on the chopping block" altogether, given Kennedy's intent to change what he calls the "broken" U.S. food system.

Cracking down on pharma

Some Wall Street analysts are less concerned about Kennedy stifling drug approvals and regulation.

"We anticipate RFK to focus on U.S. food policy and its relationship to chronic illness, not medicine," BMO Capital Markets analyst Evan Seigerman said in a note last week.

Investors are already bracing for a crackdown on food policy, with shares of processed food companies, such as PepsiCo and Coca-Cola , falling on Friday.

Wall Street has fewer immediate concerns about pharmaceutical companies. Seigerman said, "there is little precedent in recent history for HHS policy dictating or affecting FDA regulation or approval of drugs."

He added that the impact on the biotech and pharmaceutical industry is still unclear until Trump selects an FDA commissioner, and that the firm is more confident that he will tap a candidate with a "robust medical background and ties to the industry."

Getty Images

Still, Kennedy appears to favor "tighter controls and intervening a bit more" in the biotech and pharmaceutical industry, according to Dave Latshaw, co-founder and CEO of artificial intelligence drug development company BioPhy.

That could bring some uncertainty to the drug development and approval process, which poses a greater risk to companies that primarily have products in the earlier stages of development than to large pharmaceutical companies, Latshaw added.

Kennedy could attempt to crack down on the biotech and pharmaceutical industry in other ways – but they may not be successful.

He has said he wants to ban direct-to-consumer television drug advertisements. In 2023, pharmaceutical companies spent nearly $3 billion on advertising for the 10 most promoted drugs.

Experts said the First Amendment, which guarantees freedom of speech, would make that an extremely difficult task. Trump also tried to take on pharmaceutical advertising during his first administration by requiring companies to disclose the list prices of products in their ads. Drugmakers sued the government, and a federal court blocked the rule.

Kennedy's position on the drug pricing provisions in the Inflation Reduction Act, President Joe Biden's signature legislation, is unclear. That 2022 law gave Medicare the power to negotiate drug prices with manufacturers for the first time in history – a provision that the pharmaceutical industry is challenging in court.

But the Trump administration won't have much flexibility to dismantle or scale back the law without change from Congress. It also seems unlikely Kennedy would want to scrap efforts to lower drug prices, an issue top of mind for Americans, according to Amy Campbell, associate dean for law and health sciences at the University of Illinois Chicago School of Law.

Fluoride, food supply

Kennedy earlier this month proposed advising all U.S. water systems to remove fluoride from drinking water, falsely claiming that it is "an industrial waste" linked to several medical conditions, such as thyroid disease and neurodevelopmental disorders. Trump has since said that idea sounds "OK to me."

But fluoride is a naturally occurring mineral found in soil, water and plants. Adding low levels of fluoride to drinking water is widely considered one of the greatest public health achievements of the 20th century for its role in preventing tooth decay.

Campbell said the decision to add fluoride to water happens at the state and local level, so Kennedy could only advise its removal. But even that could eventually lead to certain states doing away with fluoridation, she noted.

Kennedy has been vocal about tackling the root causes of chronic diseases rather than spending resources on treating those conditions with drugs from the pharmaceutical industry. There are still few details on what exactly that would look like, but Kennedy is targeting a real issue in the U.S.

An increasing share of people in America are dealing with multiple chronic conditions, with roughly 42% having two or more, according to the CDC. More than 40% of school-aged children and adolescents have at least one.

Some of Kennedy's ideas, such as stripping ultra-processed food from school cafeterias and cracking down on food dye, have found public support on the right and left. But he has pushed misleading claims and comparisons related to food in the U.S. and how it is regulated, such as incorrectly claiming that Froot Loops cereal in Canada contains just two or three ingredients when it has 17.

Some experts said Kennedy could pressure the FDA commissioner to scrap or cut down the agency's Center for Food Safety and Applied Nutrition. But banning the use of already-approved food additives would require more rather than fewer resources, experts added. They said that the process would likely involve extensive reviews of data and real-time monitoring of the food supply, among other efforts.

Other changes may need to be spearheaded by the U.S. Department of Agriculture, which does not fall under HHS. For example, the USDA sets guidelines that govern school lunch programs.