In the first year of President Donald Trump’s second term, the U.S. Department of Health and Human Services has undergone a sweeping transformation led by health secretary Robert F. Kennedy Jr., reshaping major agencies and guidance that touch vaccination, chronic disease priorities and scientific research. Associated Press reported that Kennedy entered office in February and, within months, set off a churn across the department that supporters of his Make America Healthy Again, or MAHA, movement hailed as a needed disruption.
AP reported that Kennedy’s approach included changes that directly reached into Centers for Disease Control and Prevention guidance on vaccines. The reporting said Kennedy announced in May that the CDC would no longer recommend COVID-19 vaccines for healthy children and pregnant women, a move that AP said public health experts questioned. It also said Kennedy fired an entire 17-member CDC vaccine advisory committee in June, later installing replacements that included several vaccine skeptics—changes that AP said medical professionals found alarming.
According to AP, the advisory group’s decisions included 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. AP further reported that Kennedy in November directed the CDC to abandon its position that vaccines do not cause autism, describing the update as occurring without new evidence cited in the department’s actions.
AP also described how Kennedy’s health agenda has expanded beyond the vaccine debate into other public health and nutrition topics. It said that Kennedy has redrawn the government’s position on topics such as seed oils, fluoride and Tylenol, and that he has repeatedly used his authority to promote discredited vaccine ideas. AP reported that critics said MAHA-related calls to action that are not based on science can be dangerous, including references to promoting raw milk over pasteurized milk.
Beyond guidance changes, AP said Kennedy has reshaped HHS operations through staffing reductions and research cutbacks. The reporting said that within two months of taking office, Kennedy announced a restructuring that would shut down entire agencies, consolidate others into a new one focused on chronic disease, and lay off about 10,000 employees on top of another 10,000 who had already taken buyouts. AP said those staff reductions, along with voluntary departures, significantly thinned a department with responsibilities that include food and hospital inspections, health insurance coverage for roughly half of the country, and vaccine recommendations.
AP said Kennedy’s personnel changes also included firing or forcing out multiple leaders at HHS, including four directors at the National Institutes of Health, the FDA’s former vaccine chief, and a director of the CDC whom Kennedy had hired less than a month earlier. The reporting said the cuts also reached scientific research: AP reported that NIH slashed billions of dollars in research projects and terminated $500 million in contracts for mRNA vaccine development. AP also said Kennedy proposed or funded new research aligned with MAHA goals, including areas related to autism, Lyme disease and food additives.
Supporters of the approach have said the changes are overdue, with AP reporting that MAHA backers praised the disruption and said they had viewed HHS as corrupt and untrustworthy. AP also reported that both Democrats and Republicans applauded some agency actions, including efforts to encourage healthy eating and exercise and deals meant to lower the price of costly drugs. Still, AP said many doctors and public health experts raised “grave concerns” about the effect of the overhaul on scientific capacity.
Those concerns were voiced in AP reporting by Lawrence Gostin, a Georgetown University public health law professor who AP said was removed from a National Institutes of Health advisory board earlier this year. Gostin said, according to AP, that “At least in the immediate or intermediate future, the United States is going to be hobbled and hollowed out in its scientific leadership,” adding that he believed it would be “extraordinarily difficult to reverse all the damage.” AP reported that an HHS spokesperson, Andrew Nixon, rejected those characterizations and said HHS had advanced its work with transparency, accountability and gold-standard science.
In a statement, Nixon said the department confronted “long-standing public health challenges with transparency, courage, and gold-standard science,” and that HHS would carry that momentum into 2026, according to AP. The overhaul described by AP is unfolding alongside broader uncertainty in parts of the U.S. health system, including Medicaid cuts passed by Congress and the expiration of Affordable Care Act subsidies that AP said are putting millions of Americans’ insurance coverage in jeopardy.
Kennedy’s MAHA campaign slogan, AP reported, has also become more prominent in the broader federal government. AP said Defense Secretary Pete Hegseth appeared with Kennedy to promote fitness, Transportation Secretary Sean Duffy joined Kennedy in early December to announce $1 billion for airports to install resources such as playgrounds and nursing pods, and Environmental Protection Agency administrator Lee Zeldin said he was working toward unveiling a MAHA agenda within his own department. AP said even with that momentum, the initiative has faced stumbles, including scrutiny in May after HHS released a MAHA report that contained citations to studies that did not exist.