Since entering office in February, the health secretary has overseen a dramatic reshaping of the agencies he oversees, including eliminating thousands of jobs and freezing or canceling billions of dollars for scientific research. As part of his campaign against chronic disease, he has redrawn the government’s position on topics such as seed oils, fluoride and Tylenol. He also has repeatedly used his authority to promote discredited ideas about vaccines.

The department’s rapid transformation has garnered praise from MAHA supporters who say they long viewed HHS as corrupt and untrustworthy and have been waiting for such a disruption. And both Democrats and Republicans have applauded some of the agency’s actions, including efforts to encourage healthy eating and exercise, and deals to lower the prices of costly drugs.

But many of the drastic changes Kennedy has led at the department are raising grave concerns among doctors and public health experts.

“At least in the immediate or intermediate future, the United States is going to be hobbled and hollowed out in its scientific leadership,” said Lawrence Gostin, a Georgetown University public health law professor who was removed from a National Institutes of Health advisory board earlier this year with a letter that said he was no longer needed. “I think it will be extraordinarily difficult to reverse all the damage.”

HHS spokesperson Andrew Nixon denied any threat to scientific expertise at the agency and lauded its work.

“In 2025, the Department confronted long-standing public health challenges with transparency, courage, and gold-standard science,” Nixon said in a statement. “HHS will carry this momentum into 2026 to strengthen accountability, put patients first, and protect public health.”

The overhaul comes alongside broader uncertainties in the nation’s health system, including Medicaid cuts passed by Congress this year and expiring Affordable Care Act subsidies that are putting millions of Americans’ insurance coverage in jeopardy.

Here’s a closer look at Kennedy’s first year leading the nation’s health agency:

Kennedy’s vaccine views ripple across the department

After many years spent publicly assailing vaccines, Kennedy sought during his confirmation process to reassure senators he wouldn’t take a wrecking ball to vaccine science. But less than a year later, his health department has repeatedly pushed the limits of those commitments.

In May, Kennedy announced the Centers for Disease Control and Prevention would no longer recommend COVID-19 vaccines for healthy children and pregnant women — a move immediately questioned by public health experts who saw no new data to justify the change.

In June, Kennedy fired an entire 17-member CDC vaccine advisory committee — later installing several of his own replacements, including multiple vaccine skeptics.

That group has made decisions that have shocked medical professionals, including declining to recommend COVID-19 shots for anyone, adding new restrictions on a combination shot against chickenpox, measles, mumps and rubella and reversing the longstanding recommendation that all babies receive a hepatitis B shot at birth.

Kennedy in November also personally directed the CDC to abandon its position that vaccines do not cause autism, without supplying any new evidence to support the change. While he left the old language on the website to keep a promise he made to Republican Sen. Bill Cassidy, he added a disclaimer saying it remained because of the agreement.

Public health researchers and advocates strongly refute the updated website and note that scientists have thoroughly explored the issue in rigorous research spanning decades, all pointing to the same conclusion that vaccines don’t cause autism.

Kennedy has promised a wide-ranging effort to study environmental factors that potentially contribute to autism and in an Oval Office event with Trump in September promoted unproven and in some cases discredited ties between Tylenol, vaccines and the complex brain disorder.

Kennedy reconfigures HHS with massive staffing and research cuts

Within two months of taking office, Kennedy announced a sweeping restructuring of HHS that would shut down entire agencies, consolidate others into a new one focused on chronic disease and lay off some 10,000 employees on top of 10,000 others who had already taken buyouts.

While parts of the effort are still tied up in court, thousands of the mass layoffs were allowed to stand. Those and voluntary departures significantly thinned out the sprawling $1.7 trillion department, which oversees food and hospital inspections, health insurance for roughly half of the country and vaccine recommendations.

Kennedy also has fired or forced out several leaders at HHS, among them four directors at the National Institutes of Health, the Food and Drug Administration’s former vaccine chief and a director of the CDC whom he had hired less than a month earlier.

On top of staffing cuts, he has overseen significant cuts to scientific research. That includes NIH slashing billions of dollars in research projects and the termination of $500 million in contracts to develop vaccines using mRNA technology.

Amid the cuts, Kennedy has proposed or funded some new research on topics related to his MAHA goals, including autism, Lyme disease and food additives.

MAHA gains momentum, despite some stumbles

Kennedy started using the phrase “MAHA” on the campaign trail last year to describe his crusade against toxic exposures and childhood chronic disease, but 2025 was the year it became ingrained in the national lexicon.

In his tenure so far, the health secretary has made it the centerpiece of his work, using the MAHA branding to wage war on ultra-processed foods, pressure companies to phase out artificial food dyes, criticize fluoride in drinking water and push to ban junk food from the program that subsidizes grocery store runs for low-income Americans.

The idea has even spread beyond Kennedy’s agency across the federal government.

Defense Secretary Pete Hegseth has appeared with Kennedy to promote fitness with pull-up displays. Transportation Secretary Sean Duffy teamed up with Kennedy in early December to announce $1 billion in funding for airports to install resources like playgrounds and nursing pods for mothers and babies. And Environmental Protection Agency administrator Lee Zeldin recently announced he is working toward unveiling a MAHA agenda with health-related goals for his own department.

MAHA has earned widespread popularity among the American public — even as it has endured some administration foibles. In May, for example, HHS faced scrutiny for releasing a MAHA report that contained several citations to studies that didn’t exist.

But to the extent that the initiative has included calls to action that aren’t based on science — such as urging distrust in vaccines or promoting raw milk, which is far more likely than pasteurized milk to lead to illness — critics say it can be dangerous.