Dr. Martin Makary Chosen to Head the F.D.A.

President-elect Donald J. Trump announced on Friday that he would nominate Dr. Martin A. Makary, a Johns Hopkins University surgeon with a contrarian streak, to be commissioner of the Food and Drug Administration.

In a post on social media, Mr. Trump said: “F.D.A. has lost the trust of Americans and lost sight of its primary goal as a regulator.” He said that Dr. Makary would work under Robert F. Kennedy Jr., the president-elect’s choice for the cabinet-level role as health secretary, to “properly evaluate harmful chemicals poisoning our nation’s food supply and drugs.”

“I am confident that Dr. Makary, having dedicated his career to high-quality, lower-cost care will restore the F.D.A. to the gold standard of scientific research and cut the bureaucratic red tape at the agency to make sure Americans get the medical cures and treatments they deserve,” Mr. Trump said in a statement.

Mr. Trump announced two other top health picks on Friday evening as well. He chose Dr. Dave Weldon, a physician and former congressman from Florida, to lead the Centers for Disease Control and Prevention.

For years, Dr. Weldon championed the notion that thimerosal, a preservative once used widely in vaccines, caused an explosion of autism cases around the world. In 2007, he backed a bill proposing to take vaccine safety research out of the hands of the C.D.C. Health officials reject the idea that research shows any link between thimerosal and autism.

Mr. Trump also put forward Dr. Janette Nesheiwat, a physician and Fox News contributor, to be surgeon general. She worked caring for patients after Hurricane Katrina, an announcement from Mr. Trump said, and on the front lines of the Covid pandemic in New York City. She also markets vitamin B and vitamin C dietary supplements.

Dr. Makary, 54, rose to prominence more than a decade ago as a critic of the medical establishment, speaking out about patient safety and working with hospitals to improve practices. He also gained attention during the pandemic, weighing in on herd immunity, vaccines and masks in 2021, roiling some doctors who were still contending with packed I.C.U.s and hundreds of deaths a week.

As F.D.A. commissioner, Dr. Makary would lead an agency that has come under considerable fire from Mr. Kennedy, who would be his boss if confirmed by the Senate to become secretary of the Department of Health and Human Services.

Mr. Kennedy has been outspoken in his desire to overhaul the F.D.A., saying he would fire agency staff members who he argued had “suppressed” disputed and sometimes harmful treatments; would gut an entire department; and would clamp down on the food and pharmaceutical industries. Mr. Kennedy has also criticized the so-called user fees from drug and medical device companies that pay for thousands of employees to review industry products and account for nearly half of the agency’s overall budget of $7.2 billion.

Dr. Makary would oversee an agency that regulates a vast swath of the economy, including prescription and over-the-counter drugs, revolutionary cell and gene therapies as well as food, medical devices, tobacco and cosmetics.

The F.D.A. is supposed to ensure that the pharmaceutical supply chain is secure. It sends staff employees to inspect food and drug facilities in the United States and overseas to verify that drugs are potent and injectable therapies are sterile. The agency also oversees recalls of harmful products, including fresh produce and other foods that can become contaminated with deadly pathogens, like E. coli or listeria.

Dr. Makary is well known in certain circles. He has cultivated a high-profile public perch for criticizing government and the medical community, writing a series of books and opinion articles and appearing as a Fox News commentator on medical issues.

He ignited controversy by declaring in early 2021 that herd immunity from previous infections, or the idea that people would be broadly protected after the Omicron surge, was just weeks away, eliciting a considerable outcry from other doctors. On vaccines, he was largely opposed to mandates and also criticized the administration for minimizing the benefits of protection gained after a Covid infection over that from vaccines.

“I have argued for months that we could save more American lives if those with prior Covid-19 infection forgo vaccines until all vulnerable seniors get their first dose,” Dr. Makary wrote in an opinion article in The Wall Street Journal in 2021.

If he is confirmed by the Senate, Dr. Makary would preside over the very agency that has the primary responsibility for deciding whether to approve vaccines such as annual flu and Covid shots that are updated as the viruses mutate. The F.D.A. also evaluates continuing safety concerns for possible regulatory action. Such actions could include enhancing warnings, placing conditions on how therapies are used or even removing products from the market.

Whether Mr. Kennedy sets new parameters for vaccines — he has argued that they were not vetted properly for safety or effectiveness — could conflict with Dr. Makary’s long-held views in support of immunizations as protection against a variety of diseases. In his most recent book, Dr. Makary advocated for a universal flu vaccine that could make the shots more effective.

In recent months, Dr. Makary has publicly sought to align his views with the current pronouncements of Mr. Kennedy, who had run his own campaign for president before being embraced by Mr. Trump as a top health adviser. Dr. Makary contended that Mr. Kennedy’s skepticism about vaccines had evolved. “I would say people should not dissect what he said 30 years ago, and listen to what he’s saying now,” Dr. Makary said on Fox News on Sunday. “He’s saying very clearly he’s not anti-vax, he’s not going to remove or take away anyone’s vaccines.”

Yet Mr. Kennedy has only recently backed off his attacks on vaccines, said Dr. Paul Offit, who is the director of the Vaccine Education Center at the Children’s Hospital of Philadelphia and is an adviser to the F.D.A. Dr. Offit doubted whether Mr. Kennedy’s long-held views had changed significantly since last year, when he said on the computer scientist Lex Fridman’s podcast that there was “no vaccine that is safe and effective.” (Mr. Kennedy later said he was interrupted and meant to say no vaccine is safe and effective for everyone.)

“That somebody like Marty Makary sort of whitewashes his opinions, in order to get a position in the administration, is even more upsetting,” Dr. Offit said.

He added that Mr. Kennedy, given the power of the role he could assume as head of H.H.S., “could do an enormous amount of harm.”

Dr. Makary has worked with a Trump administration before. During Mr. Trump’s first term in office, he helped on a drug price transparency executive order and was at the White House for the signing.

Dr. Makary has also echoed Mr. Kennedy’s enthusiasm for taking a critical look at the root causes of rising rates of diseases that affect children and adults, including obesity, and increases in the incidence of cancer among young people.

Food safety and the ingredients in food have been popular targets of Mr. Kennedy, who has often said that eliminating harmful chemicals will be a major goal of his. That’s an area where the F.D.A. exercises some oversight: It regulates about 80 percent of the U.S. food supply. Food policy groups, typically aligned with Democrats, that have grown impatient with the F.D.A. have had some success in turning to the states, including California, to take up that cause in the absence of federal action.

“For the first time ever, we’re now seeing a focus on addressing the health of our nation’s children and the chronic disease epidemic,” Dr. Makary said during a post-election interview on Fox News. “And that’s exciting a lot of people.”

Mr. Kennedy’s vows to drastically alter food policy could collide with the overall missions of deregulation and cost-cutting outlined already by the incoming Trump administration, and could rile the powerful food and agricultural industries, which have stalwart Republican allies in Congress.

Another point of contention may involve the drug industry. Dr. Makary has aired concerns that Americans are too reliant on drugs, saying the nation has the most overmedicated and sickest population in the world.

“The best way to lower drug costs in the U.S. are to stop taking drugs we don’t need,” he said during a Senate round table in September.

In a note to investors, Brian Abrahams, head of global health care research with RBC Capital, said that compared with Mr. Kennedy, Dr. Makary is “less apt to dismantle” the F.D.A. and would be expected to leave core agency work to existing staff. But he added that Dr. Makary seems likely to “evolve the agency toward a more industry-unfriendly stance.”

In recent years, Dr. Makary has appeared before congressional committees as an expert reflecting Republican views. But he also has some history with Democrats: He donated $1,000 to Barack Obama’s first presidential campaign. He also serves on the board of Harrow Eye, an ophthalmology drug company, which reported paying him $40,000 in 2023.

Dr. Makary was born in England, but moved to the United States as a child and was reared in rural Pennsylvania. An accomplished surgeon and member of the elite National Academy of Medicine, Dr. Makary holds establishment credentials, including a master’s degree in public health from Harvard University. He is the Mark Ravitch chair in gastrointestinal surgery at Johns Hopkins School of Medicine, and teaches public health policy as a professor at the university’s school of public health.

Dr. Makary would succeed Dr. Robert M. Califf, who made his name as a clinical trial leader at Duke University and spoke extensively as commissioner about the danger of misinformation and the problems of high costs and chronic disease.

Sheryl Gay Stolberg and Benjamin Mueller contributed reporting.