Four months, 157 Executive Orders: Inside the science of Trump's Second Term

When Donald Trump returned to the White House in January 2025, the question wasn't whether his administration would change the direction of US health policy – it was how quickly, how deeply, and how far it would reach. In the months since, the answer has taken shape through a barrage of executive orders, high-level appointments, agency purges, and sweeping budget proposals. Taken together, they mark a radical restructuring of how the federal government defines, funds, and regulates science, medicine, and public health.

This timeline captures the most significant developments from the administration's first few months.

January 2025: The great data purge begins

Making good on his promise to move with "historic speed and strength", in his first weeks back in office President Donald Trump issued a wave of executive orders that signalled a dramatic shift in federal health and science policy – and left researchers, clinicians, and public health officials scrambling to adapt.

Among the most visible changes was a new directive recognising only two biological sexes for the purposes of federal policy. While the administration framed this as a return to "biological reality", the order immediately raised questions for researchers and health agencies tasked with studying populations that don't fit neatly into binary categories. Within days, thousands of government webpages were taken offline – including Centers for Disease Control (CDC) databases on sexual orientation and gender identity – in what critics described as a scramble to scrub terminology no longer considered acceptable under the new policy.

The administration also moved to sever long-standing global health ties, formally withdrawing the US from the World Health Organization and instructing the CDC to halt all collaboration with the agency. This followed a broader communications freeze across federal health institutions. The Department of Health and Human Services (HHS) quietly paused public-facing communications from the CDC, FDA, and NIH – effectively cutting off updates, public health guidance, and stakeholder engagement during a period of rapid change. Internally, grant review panels and advisory committees were suspended, with multiple NIH study sections cancelled with little notice.

The consequences were immediate. FDA staff removed online references to promoting diversity in clinical trials. NIH, under its newly installed acting director – Matthew Memoli, a known critic of Anthony Fauci – began terminating grants linked to diversity, equity, and inclusion (DEI) initiatives.

Critics have framed the funding freezes as a strategic lever, designed to pressure universities and research institutions to dismantle DEI infrastructure or risk losing critical federal support. At the same time, Trump reinstated a ban on federal funding for NGOs that provide abortion services, reversed a Biden-era executive order aimed at expanding abortion access, and withdrew a proposed ban on menthol cigarettes. Several federal inspectors general – including at HHS – were dismissed.

In isolation, each move could be framed as a policy pivot. Taken together, they reflect a broader recalibration of how – and for whom – American health policy is shaped. For many in the research and public health communities, January was not just the start of a new term. It was the beginning of an entirely new operating environment.

February 2025: Institutions hollowed, ideology installed

If January was about issuing orders, February showed what it means to live under them. Across the nation's health agencies and research institutions, the ripple effects of the Trump administration's early moves began turning into full-blown structural change – or, in many cases, deliberate unravelling.

The month began with widening fallout from the administration's freeze on USAID contracts, with funding to global health partners and development programmes quietly suspended or rescinded. For longtime recipients, it wasn't just a financial disruption – it signalled that the US' support for health diplomacy, maternal care, and HIV programmes abroad was being reevaluated through a political lens.

At home, the CDC's main advisory board broke ranks with the administration, calling for the restoration of scrubbed health data related to sexual orientation and gender identity – a quiet but notable act of resistance. Their request came amid mounting concern across the scientific community about the integrity and transparency of federal data.

But, while advisory boards made appeals, policy continued to accelerate in the other direction.

The Trump administration announced plans to cap what it would pay for indirect research costs – such as lab infrastructure and administrative support – at just 15% of NIH grants, a dramatic cut that alarmed universities and research hospitals across the country. Though a federal judge extended a temporary order blocking those cuts from taking immediate effect, the signal was clear: support for basic research infrastructure would no longer be assumed.

Meanwhile, the White House began notifying more than 5,000 probationary employees across health agencies that their roles would be terminated. The affected workers ranged from drug inspectors to maternal health specialists and AI researchers. Many were told they were being let go for "poor performance" – despite past performance reviews that told a different story. For agency insiders, it felt less like a routine staffing adjustment and more like ideological house cleaning.

At the NIH, turnover continued. Acting Director Lawrence Tabak was forced out. His departure followed the dismantling of several long-standing diversity programmes, including the NIH's flagship initiative to diversify the biomedical workforce and the cancellation of a parallel programme by the Howard Hughes Medical Institute – the nation's largest private funder of biomedical research.

With Tabak gone, Trump swore in Robert F. Kennedy Jr. as Secretary of Health and Human Services. The move was as symbolic as it was operational: Kennedy, a long-time vaccine sceptic, was also appointed chair of the newly formed Make America Healthy Again (MAHA) Commission, established via executive order. The commission's stated aim – promoting healthier lifestyles and chronic disease prevention – was quickly overshadowed by Kennedy's public remarks downplaying a fatal measles case in Texas. It was the first measles death in the US in over a decade. For Kennedy, the outbreak was "not unusual."

Elsewhere, meetings that had long formed the rhythm of seasonal public health response began disappearing. The FDA cancelled its advisory committee on flu strains for the next vaccine season. The CDC's vaccine advisory board postponed a key meeting. These moves, though procedural on paper, signalled deep instability in public health planning.

At the same time, the White House took more visible steps to reinforce its health agenda. Trump signed an executive order expanding access to in vitro fertilisation – a move largely seen as a political response to growing conservative scrutiny around reproductive rights. Even where the administration walked back – such as its decision to rehire FDA workers it had previously fired after pushback from industry – the message was one of volatility, not reconciliation.

By month's end, the Trump administration was touting a new executive order calling for "greater transparency" in medical pricing. But the story in February wasn't clarity – it was attrition. Not with a bang, but with memos, firings, postponed meetings, and programmes pulled offline.

March 2025: Executive orders continue to reshape health policy

By March, the Trump administration's executive orders were no longer just directives on paper – they were actively reshaping the nation's health policy landscape. Fallout from Executive Order 14210 continued as a federal judge issued a preliminary injunction blocking the administration's plan to cap indirect research costs at 15%, calling the move potentially unlawful and signalling that legal challenges to the broader research funding rollback had real teeth. The decision offered temporary relief to universities and health systems bracing for a sudden loss of overhead support – but left the long-term stability of federal research funding in question.

That uncertainty deepened when the administration abruptly cancelled over $400 million in federal grants to Columbia University. Officials declined to provide a detailed rationale, but the move came shortly before funding was also withdrawn from Columbia's long-running diabetes study – a landmark project tracking metabolic disease for more than 30 years. Researchers saw the cancellations not as coincidental, but retaliatory.

In a decision that stunned public health leaders, HHS announced that the CDC would study the long-debunked claim that vaccines are linked to autism. Around the same time, David Geier – a known vaccine critic who was previously disciplined for practising medicine without a license – was selected to lead the new study. The choice drew sharp condemnation from scientists, including former CDC officials, who warned the move could undermine decades of immunisation progress.

Inside agencies, personnel changes accelerated. Jay Bhattacharya was confirmed as NIH director and Dr Martin Makary as commissioner of the FDA, formalising the administration's realignment of science leadership. Both had built public profiles as critics of pandemic-era policies. Meanwhile, longtime NIH institute directors quietly resigned, including the head of the National Human Genome Research Institute – the first such departure since Trump's return. Susan Monarez, a relatively unknown figure in public health, was nominated to lead the Centers for Disease Control and Prevention (CDC).

The month's appointment streak was punctuated by a rare public backlash. After Peter Marks – the FDA's top vaccine regulator – was pushed out, more than 2,000 members of the National Academies of Sciences, Engineering, and Medicine signed a joint statement calling for "an immediate halt to the ongoing attack on scientific integrity."

The erosion of public health infrastructure continued. The NIH terminated several major HIV prevention grants, including projects focused on PrEP access for young adults. The VA announced plans to phase out gender-affirming care, and the HHS quietly disbanded its human research ethics advisory panel. At the same time, more than $11 billion in federal public health grants were cancelled – money originally allocated for the COVID-19 response, now redirected or removed despite being used to track disease, expand addiction treatment, and respond to the measles outbreak in Texas.

April 2025: "Liberation Day" and the blunt force of tariffs

On 1st April, the Trump administration marked what it called "Liberation Day" – not a holiday, nor an April Fools prank, but a declaration of victory over what it described as bureaucratic overreach, academic elitism, and "woke science". In practice, it kicked off the most aggressive month yet in the administration's campaign to remake the American health system by executive fiat.
That blunt-force approach was on full display.

On the first official day of Makary's tenure as FDA commissioner, multiple senior regulatory officials were dismissed – a move widely interpreted as a loyalty purge. Days later, Makary announced the FDA would remove non-voting industry representatives from advisory committees, a decision that further unnerved a workforce already reeling from layoffs and backlogged approvals. At least one rare disease drug approval was delayed this month, with sources tracing the delay directly to the loss of experienced staff. Makary gave his own take on those personnel changes recently on stage at BIO 2025.

Elsewhere, the White House Office of Management and Budget made headlines when a leaked internal document revealed plans to consolidate the NIH into just eight centres and slash its funding by 40%. While officials claimed the move would create "efficiencies", health leaders across the political spectrum warned that such a cut would devastate biomedical research infrastructure for a generation.

In parallel, the "Defend the Spend" initiative quietly took hold across HHS agencies. A new process now required federal officials to personally review and sign off on all NIH drawdown requests – including routine payments for already-awarded grants – leading to widespread delays in funding and administrative paralysis.

And then came the executive orders.

One of the most consequential targeted what it called "DEI-based standards" in medical education. The order instructed accrediting bodies to eliminate consideration of diversity, equity, or inclusion from medical school and residency evaluations – a move with immediate implications for physician training pipelines. Critics warned the order would undermine workforce equity and patient trust; supporters argued it would restore "merit-based" education.

Another EO, this time focused on drug pricing, was cast as a sweeping reform. It tasked HHS, CMS, and other agencies with stabilising Part D premiums, cracking down on PBMs, improving OTC pathways, reimportation, and – most notably – "ending the pill penalty" by aligning biologics and small molecule drugs under the IRA's Medicare negotiation timeline.

But here's the fine print: the order didn't say small molecule protections would be extended – only that "alignment" was needed and that any change would need to go through Congress. So, while the White House floated the language of fairness, the math still leans toward reducing protections, not extending them. Investors noticed.

Meanwhile, tariff policy began to bite. The administration launched a formal probe into pharmaceutical imports – a clear signal that drug tariffs are on the table. The medtech sector was already scrambling, with analysts warning that the proposed tariffs would cancel out biosimilar discounts and drive up prices for US consumers.

Further downstream, Medicare quietly withdrew a Biden-era plan to cover GLP-1 drugs for weight loss. Although demand for drugs like Wegovy has exploded, the administration cited "budget discipline" – despite also floating a new payment model for high-cost drugs in seniors. Internally, officials were asked to "minimise innovation disruption," even as funding cuts and regulatory chaos made that increasingly theoretical.

On the research front, April brought new tremors. The Women's Health Initiative, a multi-decade programme that shaped care for menopause and osteoporosis, announced it would lose its HHS funding in September. Days later, under political pressure, HHS reversed course, promising to "work to fully restore funding" – a rare walk-back amid a sea of cuts. Also imperiled: autism research. In a televised Cabinet meeting, HHS Secretary Robert F. Kennedy Jr told President Trump the department would undertake a "massive testing effort" to determine what causes autism.

The science community, meanwhile, found itself on the defensive. Journals reported receiving letters from federal attorneys alleging editorial bias. A Senate Appropriations hearing turned heated as Republican Senator Susan Collins rebuked the White House for gutting research and cancelling grants. She was joined by a bipartisan group calling for a reversal – a rare show of congressional unity in a deeply polarised climate.

In a final note of confusion, the administration's legal team filed an appeal after a federal judge blocked the NIH indirect cost cap, arguing that the executive branch retains authority to restructure grants. The appeal offered a preview of the next battleground: the courts.

May 2025: Global retreat, domestic realignment

By May, the Trump administration's health policy agenda had fully turned outward – or rather, inward. A month defined by executive orders, proposed budget cuts, and headline-grabbing announcements laid bare a new operating thesis: America should no longer pay more, do more, or lead more than absolutely necessary – particularly when it comes to public health and scientific research.

One of the most consequential moves came from the NIH, which announced it would terminate billions of dollars in funding for research institutions based outside the US the policy – framed as prioritising "American taxpayers" – effectively ended NIH partnerships with foreign hospitals and universities, many of which had been long-standing collaborators on global health, cancer, and infectious disease studies. For international research communities, the message was unmistakable: the US was exiting the stage.

If that decision was a cold shoulder, the proposed 2026 federal budget was a sledgehammer. The "skinny budget", released by the White House in early May, outlined sweeping cuts to the Department of Health and Human Services, including dramatic reductions for NIH and CDC. Sudip Parikh, CEO of the American Association for the Advancement of Science, called the proposal "catastrophic", warning that it would endanger US global leadership in R&D and signal the country's formal retreat from the research frontier.

Meanwhile, the FDA announced it would expand unannounced inspections of overseas manufacturing facilities, bringing foreign suppliers in line with domestic scrutiny. The agency's rationale: ensure equal treatment and avoid the perception of regulatory loopholes.

That tone sharpened with a new executive order on most-favoured nation pricing, in which President Trump declared the US would no longer "subsidise the healthcare of foreign countries." Under the order, HHS and CMS were instructed to:

• Benchmark US drug prices to those paid by other countries within 30 days.
• Enable direct-to-consumer purchases from manufacturers that comply.
• Launch rulemaking to enforce pricing compliance and review drug export practices.
• Consider revoking approvals for drugs deemed "unsafe, ineffective, or improperly marketed."
• Crack down on what the order called "global freeloading and price discrimination."

The order raised immediate alarms among economists and trade analysts, who warned that such aggressive benchmarking could trigger supply disruptions or retaliatory export limits. For the biopharma sector, the message was clear: play by Washington's rules, or prepare for scrutiny – and maybe a tariff.

That possibility grew more likely as the White House continued its probe into pharmaceutical imports, widely seen as a prelude to medicine-specific tariffs. Industry leaders pointed out that US patients – not foreign governments – were likely to bear the brunt of higher costs. The administration disagreed.

By the end of the month, the message was consistent across every policy channel: global collaboration, multilateral pricing, and open-ended public investment were no longer guaranteed.

But the White House’s efforts to reshape the global economic playing field met new resistance. In a major blow to one of President Trump’s cornerstone policies, the US Court of International Trade blocked the administration’s sweeping global trade tariffs, ruling that the emergency law used to justify the measures did not give the president unilateral authority to impose tariffs on nearly every country. The court emphasised that under the Constitution, the power to regulate foreign commerce lies squarely with Congress. Within minutes, the administration vowed to appeal.

It was a rare and public legal rebuke – and a reminder that, while executive orders can move fast, they don’t move unchallenged.